Test A-Z

1) Liquid Biopsy (CTC):

Liquid biopsy, specifically the detection of circulating tumor cells (CTCs), is a non-invasive diagnostic technique used in oncology to assess and monitor cancer. Unlike traditional tissue biopsies, which involve the removal of a sample of the tumor or affected tissue, liquid biopsies involve the analysis of various components in a patient’s bodily fluids, such as blood or urine, to gather information about the presence and characteristics of cancer cells.

Here are some key points about liquid biopsy, particularly in the context of CTCs:

1) Circulating Tumor Cells (CTCs): CTCs are cancer cells that have detached from the primary tumor or metastatic sites and entered the bloodstream. These cells can travel through the bloodstream to other parts of the body and potentially form new tumors, a process known as metastasis. CTCs can carry valuable information about the primary tumor’s genetic mutations and characteristics.

2) Purpose of CTC Detection: The detection and analysis of CTCs serve several purposes in cancer care:

Early Detection: Liquid biopsies can help detect cancer at an early stage, potentially before symptoms develop.
Treatment Monitoring: CTC analysis can be used to monitor the effectiveness of cancer treatment, such as chemotherapy or targeted therapy.
Assessing Disease Progression: Changes in CTC levels and characteristics can provide insights into disease progression or recurrence.
Personalized Medicine: CTC analysis can help guide treatment decisions by identifying specific genetic mutations or biomarkers associated with the cancer, allowing for targeted therapies.

Methods of CTC Detection: Various techniques are used to isolate and detect CTCs from a patient’s blood sample. These methods include immunomagnetic separation, microfluidic devices, and polymerase chain reaction (PCR) to amplify and analyze specific DNA or RNA markers.

2) Her2-neu by FISH:

HER2/neu (Human Epidermal Growth Factor Receptor 2), also known as ERBB2, is a gene that encodes a protein involved in cell growth and division. In breast cancer and some other types of cancer, the HER2/neu gene can be amplified or overexpressed, leading to uncontrolled cell growth and an aggressive cancer phenotype. Testing for HER2/neu status is crucial in breast cancer diagnosis and treatment planning. Fluorescence In Situ Hybridization (FISH) is one of the methods used to determine the HER2/neu status in breast cancer. Here’s how HER2/neu testing by FISH works:

Sample Collection: A tissue sample (usually from a biopsy or surgical resection of the tumor) is collected from the patient.
Tissue Preparation: The tissue sample is processed and prepared for FISH analysis. This often involves fixing the tissue and preparing thin slices on glass slides.
FISH Probe Preparation: In FISH, specific DNA probes are used to target and bind to the HER2/neu gene region. These probes are designed to bind to the HER2/neu gene or the adjacent chromosome region.
Hybridization: The prepared tissue sample is exposed to the DNA probes. If the HER2/neu gene is amplified (meaning there are more copies of it than usual), the probes will bind to these extra copies.
Fluorescent Labeling: The DNA probes used in FISH are typically labeled with fluorescent molecules. When these probes bind to the target DNA sequences, they emit fluorescence, allowing for visualization.
Imaging and Analysis: The tissue sample is examined under a fluorescent microscope. The presence and number of fluorescent signals associated with the HER2/neu gene are assessed. If there is an increased number of HER2/neu gene copies (usually defined as HER2/neu gene amplification), it indicates a positive HER2 status.

3) C-MYC FISH:

C-MYC (also known as MYC) is a proto-oncogene that plays a critical role in the regulation of cell growth and proliferation. Abnormalities in the C-MYC gene, such as gene amplification or translocation, are associated with the development of various cancers, including lymphomas, leukemias, and some solid tumors. Fluorescence In Situ Hybridization (FISH) is a molecular diagnostic technique used to detect and assess C-MYC abnormalities in cancer cells. Here’s how C-MYC testing by FISH works:

Sample Collection: A tissue sample, typically obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains cancer cells.
Tissue Preparation: The collected tissue sample is processed and prepared for FISH analysis. This may involve fixing the tissue and preparing thin sections on glass slides.
FISH Probe Preparation: Specific DNA probes are designed to target the C-MYC gene region. These probes are labeled with fluorescent molecules that emit distinct colors when exposed to specific wavelengths of light.
Hybridization: The tissue sample is incubated with the DNA probes. If there are abnormalities in the C-MYC gene, such as amplification or translocation, the DNA probes will bind to the corresponding target sequences.
Fluorescent Labeling: When the DNA probes bind to the target C-MYC gene sequences, they emit fluorescent signals. These signals can be visualized and analyzed using a fluorescent microscope.
Imaging and Analysis: The tissue sample is examined under the fluorescent microscope. The number and pattern of fluorescent signals are assessed. Abnormalities, such as C-MYC gene amplification or translocation, are identified based on the presence of extra copies of the C-MYC gene or its fusion with another gene.

C-MYC FISH testing is particularly important in the diagnosis and management of certain cancers, including Burkitt lymphoma and some types of B-cell lymphomas. C-MYC abnormalities are associated with aggressive tumor behavior and can influence treatment decisions. For example, in Burkitt lymphoma, C-MYC translocation is a hallmark genetic alteration, and identifying this alteration can be essential for diagnosis and guiding treatment. The results of C-MYC FISH testing provide valuable information about the genetic characteristics of cancer cells. These results can help oncologists determine the most appropriate treatment strategies, including whether targeted therapies or specific chemotherapy regimens are needed to address the C-MYC abnormality.

4) BCL-6 by FISH:

BCL-6 (B-cell lymphoma 6) is a gene associated with the development of various lymphomas, especially B-cell non-Hodgkin lymphomas (NHL). Abnormalities in the BCL-6 gene, such as translocations or gene rearrangements, are often observed in these lymphomas. Fluorescence In Situ Hybridization (FISH) is a molecular technique used to detect and assess BCL-6 gene abnormalities in cancer cells. Here’s how BCL-6 testing by FISH works:

Sample Collection: A tissue sample, typically obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains lymphoma cells.
Tissue Preparation: The collected tissue sample is processed and prepared for FISH analysis. This may involve fixing the tissue and preparing thin sections on glass slides.
FISH Probe Preparation: Specific DNA probes are designed to target the BCL-6 gene region. These probes are labeled with fluorescent molecules that emit distinct colors when exposed to specific wavelengths of light.
Hybridization: The tissue sample is incubated with the DNA probes. If there are abnormalities in the BCL-6 gene, such as translocations or rearrangements, the DNA probes will bind to the corresponding target sequences.
Fluorescent Labeling: When the DNA probes bind to the target BCL-6 gene sequences, they emit fluorescent signals. These signals can be visualized and analyzed using a fluorescent microscope.

Imaging and Analysis: The tissue sample is examined under the fluorescent microscope. The number and pattern of fluorescent signals are assessed. Abnormalities, such as BCL-6 gene translocation or rearrangement, are identified based on the presence of altered patterns of fluorescence signals.

The results of BCL-6 FISH testing provide valuable information about the genetic characteristics of lymphoma cells. These results can help guide treatment decisions, including the selection of specific therapies or the assessment of the lymphoma’s aggressiveness.

5) BCL-2 by FISH:

BCL-2 (B-cell lymphoma 2) is a gene associated with the regulation of apoptosis (programmed cell death) in cells. Abnormalities in the BCL-2 gene, such as translocations or gene rearrangements, are frequently found in various types of lymphomas, particularly B-cell non-Hodgkin lymphomas (NHL). Fluorescence In Situ Hybridization (FISH) is a molecular technique used to detect and assess BCL-2 gene abnormalities in cancer cells. Here’s how BCL-2 testing by FISH works:

Sample Collection: A tissue sample, typically obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains lymphoma cells.
Tissue Preparation: The collected tissue sample is processed and prepared for FISH analysis. This may involve fixing the tissue and preparing thin sections on glass slides.
FISH Probe Preparation: Specific DNA probes are designed to target the BCL-2 gene region. These probes are labeled with fluorescent molecules that emit distinct colors when exposed to specific wavelengths of light.
Hybridization: The tissue sample is incubated with the DNA probes. If there are abnormalities in the BCL-2 gene, such as translocations or rearrangements, the DNA probes will bind to the corresponding target sequences.
Fluorescent Labeling: When the DNA probes bind to the target BCL-2 gene sequences, they emit fluorescent signals. These signals can be visualized and analyzed using a fluorescent microscope.
Imaging and Analysis: The tissue sample is examined under the fluorescent microscope. The number and pattern of fluorescent signals are assessed. Abnormalities, such as BCL-2 gene translocation or rearrangement, are identified based on the presence of altered patterns of fluorescence signals.

BCL-2 FISH testing is particularly important in the diagnosis and classification of various B-cell NHL subtypes. Different subtypes of B-cell NHL can have distinct genetic alterations, and the detection of BCL-2 gene abnormalities can help pathologists and oncologists refine their diagnosis and treatment strategies.

For example, the t(14;18) translocation, which involves the BCL-2 gene, is a hallmark genetic alteration in follicular lymphoma. Detecting this translocation can aid in confirming the diagnosis of follicular lymphoma and may have implications for treatment decisions.

The results of BCL-2 FISH testing provide valuable information about the genetic characteristics of lymphoma cells. These results can help guide treatment decisions, including the selection of specific therapies or the assessment of the lymphoma’s aggressiveness.

6) ALK by FISH:

ALK (Anaplastic Lymphoma Kinase) is a gene associated with the development of certain cancers, including non-small cell lung cancer (NSCLC) and anaplastic large cell lymphoma (ALCL). Abnormalities in the ALK gene, such as gene rearrangements or translocations, can lead to the overactivation of the ALK protein, promoting uncontrolled cell growth and cancer development. Fluorescence In Situ Hybridization (FISH) is a molecular technique used to detect and assess ALK gene abnormalities in cancer cells. Here’s how ALK testing by FISH works:

Sample Collection: A tissue sample, typically obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains cancer cells.
Tissue Preparation: The collected tissue sample is processed and prepared for FISH analysis. This may involve fixing the tissue and preparing thin sections on glass slides.
FISH Probe Preparation: Specific DNA probes are designed to target the ALK gene region. These probes are labeled with fluorescent molecules that emit distinct colors when exposed to specific wavelengths of light.
Hybridization: The tissue sample is incubated with the DNA probes. If there are abnormalities in the ALK gene, such as translocations or rearrangements, the DNA probes will bind to the corresponding target sequences.
Fluorescent Labeling: When the DNA probes bind to the target ALK gene sequences, they emit fluorescent signals. These signals can be visualized and analyzed using a fluorescent microscope.
Imaging and Analysis: The tissue sample is examined under the fluorescent microscope. The number and pattern of fluorescent signals are assessed. Abnormalities, such as ALK gene rearrangements, are identified based on the presence of altered patterns of fluorescence signals.

ALK FISH testing is particularly important in the diagnosis and treatment of NSCLC and ALCL. In NSCLC, the detection of ALK gene rearrangements is crucial for identifying patients who may benefit from targeted therapies, such as ALK inhibitors like crizotinib, alectinib, or ceritinib. These drugs are specifically designed to block the activity of the overactive ALK protein and can lead to improved treatment outcomes in patients with ALK-positive NSCLC.

In ALCL, ALK gene rearrangements are a hallmark genetic alteration and play a key role in the diagnosis of this subtype of lymphoma. Confirming the presence of ALK gene abnormalities can aid in the accurate diagnosis and classification of the lymphoma, which can have implications for treatment decisions.

The results of ALK FISH testing provide critical information about the genetic characteristics of cancer cells and help guide treatment decisions. As with other FISH tests, the interpretation of ALK FISH results should be performed by experienced pathologists or oncologists who are familiar with the clinical context and guidelines for the specific cancer being evaluated. The results are often used in combination with other diagnostic and prognostic factors to tailor treatment plans for individual patients.

7) ROS1 by FISH:

ROS1 (c-ros oncogene 1) is a gene that encodes a receptor tyrosine kinase. Abnormalities in the ROS1 gene, such as gene rearrangements, are associated with certain types of cancer, particularly non-small cell lung cancer (NSCLC). Fluorescence In Situ Hybridization (FISH) is a molecular technique used to detect and assess ROS1 gene rearrangements in cancer cells. Here’s how ROS1 testing by FISH works:

Sample Collection: A tissue sample, typically obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains cancer cells.
Tissue Preparation: The collected tissue sample is processed and prepared for FISH analysis. This may involve fixing the tissue and preparing thin sections on glass slides.
FISH Probe Preparation: Specific DNA probes are designed to target the ROS1 gene region. These probes are labeled with fluorescent molecules that emit distinct colors when exposed to specific wavelengths of light.
Hybridization: The tissue sample is incubated with the DNA probes. If there are abnormalities in the ROS1 gene, such as rearrangements or fusions with other genes, the DNA probes will bind to the corresponding target sequences.
Fluorescent Labeling: When the DNA probes bind to the target ROS1 gene sequences, they emit fluorescent signals. These signals can be visualized and analyzed using a fluorescent microscope.
Imaging and Analysis: The tissue sample is examined under the fluorescent microscope. The number and pattern of fluorescent signals are assessed. Abnormalities, such as ROS1 gene rearrangements, are identified based on the presence of altered patterns of fluorescence signals.

ROS1 FISH testing is particularly important in the diagnosis and treatment of NSCLC. ROS1 gene rearrangements are relatively rare but are considered a driver mutation in a subset of NSCLC cases. Detecting ROS1 gene rearrangements is crucial for identifying patients who may benefit from targeted therapies, such as ROS1 inhibitors like crizotinib, entrectinib, or ceritinib. These drugs are specifically designed to block the activity of the overactive ROS1 protein and can lead to improved treatment outcomes in patients with ROS1-positive NSCLC.

The results of ROS1 FISH testing provide critical information about the genetic characteristics of cancer cells and help guide treatment decisions. As with other FISH tests, the interpretation of ROS1 FISH results should be performed by experienced pathologists or oncologists who are familiar with the clinical context and guidelines for the specific cancer being evaluated. The results are often used in combination with other diagnostic and prognostic factors to tailor treatment plans for individual patients.

8) ROS1 by FISH:

Sample Collection: A tissue sample, typically obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains cancer cells.
Tissue Preparation: The collected tissue sample is processed and prepared for FISH analysis. This may involve fixing the tissue and preparing thin sections on glass slides.
FISH Probe Preparation: Specific DNA probes are designed to target the ROS1 gene region. These probes are labeled with fluorescent molecules that emit distinct colors when exposed to specific wavelengths of light.
Hybridization: The tissue sample is incubated with the DNA probes. If there are abnormalities in the ROS1 gene, such as rearrangements or fusions with other genes, the DNA probes will bind to the corresponding target sequences.
Fluorescent Labeling: When the DNA probes bind to the target ROS1 gene sequences, they emit fluorescent signals. These signals can be visualized and analyzed using a fluorescent microscope.
Imaging and Analysis: The tissue sample is examined under the fluorescent microscope. The number and pattern of fluorescent signals are assessed. Abnormalities, such as ROS1 gene rearrangements, are identified based on the presence of altered patterns of fluorescence signals.

9) N-MYC by FISH:

N-MYC (Neuroblastoma Myc) is a gene that plays a critical role in the regulation of cell growth and proliferation. Abnormalities in the N-MYC gene, such as gene amplification, are associated with the development of neuroblastoma, a childhood cancer that arises from immature nerve cells. Fluorescence In Situ Hybridization (FISH) is a molecular technique used to detect and assess N-MYC gene amplification in cancer cells, particularly in neuroblastoma. Here’s how N-MYC testing by FISH works:

Sample Collection: A tissue sample, typically obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains neuroblastoma cells.
Tissue Preparation: The collected tissue sample is processed and prepared for FISH analysis. This may involve fixing the tissue and preparing thin sections on glass slides.
FISH Probe Preparation: Specific DNA probes are designed to target the N-MYC gene region. These probes are labeled with fluorescent molecules that emit distinct colors when exposed to specific wavelengths of light.
Hybridization: The tissue sample is incubated with the DNA probes. If there is gene amplification in the N-MYC gene, meaning there are extra copies of it, the DNA probes will bind to the corresponding target sequences.
Fluorescent Labeling: When the DNA probes bind to the target N-MYC gene sequences, they emit fluorescent signals. These signals can be visualized and analyzed using a fluorescent microscope.
Imaging and Analysis: The tissue sample is examined under the fluorescent microscope. The number and pattern of fluorescent signals are assessed. The presence of multiple copies of the N-MYC gene, indicative of gene amplification, is identified based on the altered patterns of fluorescence signals.

N-MYC FISH testing is particularly important in the diagnosis and risk stratification of neuroblastoma, a cancer that affects children, often in early childhood. Gene amplification of N-MYC is associated with a more aggressive form of the disease and poorer prognosis. Detecting N-MYC gene amplification helps oncologists determine the appropriate treatment plan and predict the likelihood of the cancer responding to therapy.

The results of N-MYC FISH testing provide valuable information about the genetic characteristics of neuroblastoma cells and can guide treatment decisions. For patients with N-MYC-amplified neuroblastoma, more intensive therapies may be considered to improve treatment outcomes.

As with other FISH tests, the interpretation of N-MYC FISH results should be performed by experienced pathologists or oncologists who are familiar with the clinical context and guidelines for neuroblastoma. The results are often used in combination with other diagnostic and prognostic factors to tailor treatment plans for individual patients.

10) Combo MYC & BCL2 by FISH:

Combining MYC and BCL2 testing by FISH (Fluorescence In Situ Hybridization) is a molecular diagnostic approach used to assess the genetic abnormalities in cancer cells, particularly in lymphomas and some types of solid tumors. This combined FISH analysis involves the evaluation of two different genes: MYC (c-Myc) and BCL2 (B-cell lymphoma 2), both of which are involved in cell growth and apoptosis regulation. Here’s how the combination of MYC and BCL2 testing by FISH typically works:

Sample Collection: A tissue sample, often obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains cancer cells.
Tissue Preparation: The collected tissue sample is processed and prepared for FISH analysis. This includes fixing the tissue and preparing thin sections on glass slides.
FISH Probe Preparation: Specific DNA probes are designed to target the MYC gene region and the BCL2 gene region. These probes are labeled with distinct fluorescent molecules that emit different colors when exposed to specific wavelengths of light. The MYC probe is usually labeled with one color, while the BCL2 probe is labeled with another color
Hybridization: The tissue sample is incubated with both the MYC and BCL2 DNA probes. If there are abnormalities in either the MYC or BCL2 genes, such as gene rearrangements or amplifications, the corresponding DNA probes will bind to the target sequences.
Fluorescent Labeling: When the DNA probes bind to the target MYC and BCL2 gene sequences, they emit fluorescent signals in their respective colors.
Imaging and Analysis: The tissue sample is examined under a fluorescent microscope, which can distinguish between the different fluorescent signals emitted by the MYC and BCL2 probes. The presence of altered patterns of fluorescence signals in either the MYC or BCL2 genes indicates genetic abnormalities, such as translocations, rearrangements, or amplifications.

The combined MYC and BCL2 FISH analysis is particularly important in the diagnosis and classification of various types of lymphomas, such as double-hit lymphomas. These lymphomas are characterized by concurrent MYC and BCL2 gene abnormalities and are associated with aggressive disease behavior.

In addition to diagnosis, this combined FISH analysis can help guide treatment decisions. For example, lymphomas with both MYC and BCL2 abnormalities may require more intensive therapies or different treatment approaches than lymphomas with a single gene abnormality.

As with other FISH tests, the interpretation of combined MYC and BCL2 FISH results should be conducted by experienced pathologists or oncologists who are familiar with the clinical context and guidelines for the specific cancer being evaluated. These results are often used in conjunction with other diagnostic and prognostic factors to tailor treatment plans for individual patients.

11) 1p/19q codeletion:

1p/19q codeletion analysis by FISH (Fluorescence In Situ Hybridization) is a molecular diagnostic technique used primarily in the diagnosis and classification of a type of brain tumor known as an oligodendroglioma. The presence or absence of a codeletion of the short arm of chromosome 1 (1p) and the long arm of chromosome 19 (19q) is a key genetic feature that distinguishes oligodendrogliomas and can provide important prognostic information. Here’s how 1p/19q codeletion analysis by FISH typically works:

Sample Collection: A tissue sample, typically obtained through a brain biopsy or surgical resection, is collected from the patient. This tissue sample contains tumor cells.
Tissue Preparation: The collected tissue sample is processed and prepared for FISH analysis. This may involve fixing the tissue and preparing thin sections on glass slides.
FISH Probe Preparation: Specific DNA probes are designed to target the 1p and 19q regions of the chromosomes. These probes are labeled with fluorescent molecules that emit distinct colors when exposed to specific wavelengths of light. One probe is designed to bind to the 1p region, and another is designed to bind to the 19q region.
Hybridization: The tissue sample is incubated with both the 1p and 19q DNA probes. If there is a codeletion of both 1p and 19q, meaning both regions are missing or deleted in the tumor cells, the corresponding DNA probes will bind to the remaining target sequences.
Fluorescent Labeling: When the DNA probes bind to the target 1p and 19q gene sequences, they emit fluorescent signals in their respective colors.
Imaging and Analysis: The tissue sample is examined under a fluorescent microscope, which can distinguish between the different fluorescent signals emitted by the 1p and 19q probes. The presence or absence of a codeletion is determined based on the patterns of fluorescence signals. If both 1p and 19q regions are deleted in the tumor cells, it indicates a codeletion.

The presence of a 1p/19q codeletion is considered a molecular hallmark of oligodendrogliomas and can aid in distinguishing these tumors from other types of brain tumors. Oligodendrogliomas with a 1p/19q codeletion tend to have a better response to certain treatments, such as chemotherapy with agents like PCV (procarbazine, lomustine, and vincristine), and a more favorable prognosis compared to those without the codeletion.

The results of 1p/19q codeletion analysis by FISH provide critical information for tumor classification and treatment planning for patients with oligodendrogliomas. The interpretation of these results should be conducted by experienced pathologists or molecular geneticists who are familiar with the clinical context and guidelines for brain tumor diagnosis. The results are often used in conjunction with other diagnostic and prognostic factors to develop individualized treatment strategies.

11) Diffuse large B cell lymphoma:

Fluorescence In Situ Hybridization (FISH) can be used to analyze genetic abnormalities in diffuse large B-cell lymphoma (DLBCL), which is the most common type of non-Hodgkin lymphoma. FISH analysis in DLBCL is performed to detect specific genetic alterations that can have diagnostic, prognostic, and treatment implications. Here are some of the key genetic abnormalities that can be assessed in DLBCL using FISH:

MYC Rearrangement: MYC (c-Myc) is an oncogene involved in cell growth and proliferation. In DLBCL, rearrangements of the MYC gene can occur, which can lead to more aggressive disease. Detection of MYC rearrangements using FISH is essential for diagnosing double-hit or triple-hit lymphomas, which have MYC rearrangements along with rearrangements of other genes like BCL2 and/or BCL6.
BCL2 and BCL6 Rearrangements: BCL2 and BCL6 are genes also associated with lymphomas. Rearrangements of these genes can have prognostic significance in DLBCL. For example, the presence of a BCL2 rearrangement, when combined with MYC rearrangement, can indicate a double-hit lymphoma.
IGH Translocations: FISH can be used to detect translocations of immunoglobulin heavy chain (IGH) gene regions. These translocations can involve various partner genes and play a role in lymphomagenesis. IGH translocations can help classify DLBCL into different subtypes.
Other Genetic Abnormalities: FISH can be used to assess other genetic alterations in DLBCL, such as amplifications or deletions of specific genes or gene regions, which can have diagnostic and prognostic significance.

The specific FISH probes used in DLBCL testing depend on the suspected genetic abnormalities and the clinical context. The results of FISH testing can provide information about the genetic characteristics of the tumor cells and help guide treatment decisions.

DLBCL is a heterogeneous disease, and understanding the genetic profile of the tumor can be crucial for selecting the most appropriate treatment approach. For example, certain DLBCL subtypes with specific genetic alterations may respond better to targeted therapies or more intensive chemotherapy regimens.

Interpretation of FISH results in DLBCL should be carried out by experienced pathologists or molecular geneticists who are familiar with the clinical context and guidelines for DLBCL diagnosis and classification. These results are often integrated with other clinical and pathological factors to develop personalized treatment plans for DLBCL patients.

Breast biopsy with ER, PR & Her-2:

A breast biopsy with ER (estrogen receptor), PR (progesterone receptor), and HER2 (human epidermal growth factor receptor 2) testing is a diagnostic procedure used to determine certain characteristics of breast cancer cells. These tests provide important information that helps guide treatment decisions and prognosis in breast cancer patients.

Here’s how the biopsy and testing process typically works:

Biopsy: The process begins with a breast biopsy. During a biopsy, a small sample of breast tissue is removed and sent to a pathology laboratory for examination. There are different methods for breast biopsy, including core needle biopsy and surgical biopsy, depending on the specific circumstances of the patient and the lesion being investigated.
Tissue Preparation: In the pathology laboratory, the tissue sample obtained from the biopsy is processed and prepared for analysis. Thin sections of the tissue are typically placed on glass slides for further testing.
Immunohistochemistry (IHC): IHC is a common technique used to assess the expression of estrogen receptors (ER) and progesterone receptors (PR) in breast cancer cells. Antibodies that specifically bind to ER and PR proteins are applied to the tissue samples. If the cancer cells express these receptors, they will bind to the antibodies, resulting in a visible color change that can be detected under a microscope.

- ER Positive (ER+): If the cancer cells express estrogen receptors, they are considered ER-positive. This information is important because it indicates that the cancer may respond to hormonal therapies like tamoxifen or aromatase inhibitors.
- PR Positive (PR+): The presence of progesterone receptors in cancer cells is indicative of PR-positive breast cancer. PR positivity can also influence treatment decisions regarding hormonal therapy.

HER2 Testing: HER2 testing is typically performed using either immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH) techniques. HER2-positive breast cancer means that the HER2 protein is overexpressed or that the HER2 gene is amplified in cancer cells.

- HER2 Positive (HER2+): HER2-positive breast cancer is associated with a more aggressive tumor behavior. However, it can be treated with targeted therapies such as trastuzumab (Herceptin) or other HER2-targeted drugs.

The results of these tests are crucial for several reasons:

They help determine the subtype of breast cancer, such as ER-positive, PR-positive, HER2-positive, or triple-negative breast cancer.
They guide treatment decisions. ER and PR-positive cancers may respond to hormonal therapy, while HER2-positive cancers may require targeted therapies in addition to standard treatments.
They provide prognostic information and can help predict the likelihood of disease recurrence.

The combination of these receptor tests helps oncologists create a personalized treatment plan tailored to the specific characteristics of the patient’s breast cancer. This approach aims to optimize treatment efficacy while minimizing potential side effects.

Her2-neu by IHC:

HER2/neu (Human Epidermal Growth Factor Receptor 2), also known as HER2, is a protein that plays a role in the regulation of cell growth and division. In breast cancer and some other types of cancer, the HER2 gene can be amplified or overexpressed, leading to uncontrolled cell growth and an aggressive cancer phenotype. Immunohistochemistry (IHC) is a common diagnostic test used to assess HER2 protein expression in cancer tissue. Here’s how HER2/neu testing by IHC works:

Sample Collection: A tissue sample, typically obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains cancer cells.
Tissue Preparation: The collected tissue sample is processed and prepared for IHC analysis. This may involve fixing the tissue and preparing thin sections on glass slides.
IHC Staining: Specific antibodies designed to target the HER2 protein are applied to the tissue sections. These antibodies are tagged with a colored or fluorescent label. If HER2 protein is present in the cancer cells, the antibodies will bind to it.
Visualization: After the antibodies have been applied and allowed to bind to the HER2 protein, the tissue sections are examined under a microscope. If HER2 protein is present and overexpressed in the cancer cells, it will be visible as staining within the cells.
Scoring: The results of the HER2/neu IHC test are typically scored using a scale that ranges from 0 to 3+:

- 0 (Negative): No HER2 protein expression or only minimal expression in less than 10% of cells.
- 1+ (Negative): Faint or barely perceptible staining in more than 10% of cells.
- 2+ (Indeterminate): Weak to moderate staining in more than 10% of cells.
- 3+ (Positive): Strong, complete membrane staining in more than 10% of cells. This indicates HER2 protein overexpression.

HER2/neu IHC results with a score of 3+ are considered positive and indicate HER2 protein overexpression. This is a key marker for HER2-positive breast cancer and certain other cancers. HER2-positive status can influence treatment decisions, as patients with HER2-positive cancer may benefit from targeted therapies such as trastuzumab (Herceptin) or other HER2-targeted drugs.

It’s important to note that HER2/neu IHC testing is often followed by confirmatory testing using fluorescence in situ hybridization (FISH) or other molecular techniques to further assess HER2 gene amplification. This additional testing helps ensure accurate HER2 status determination, as not all tumors with HER2 protein overexpression have gene amplification.

Interpretation of HER2/neu IHC results should be performed by experienced pathologists who are familiar with the scoring criteria and guidelines established by organizations like the American Society of Clinical Oncology (ASCO) and the College of American Pathologists (CAP). Accurate HER2 testing is vital for personalized cancer treatment planning.

Ki-67(Mib-1) By IHC:

Ki-67, also known as MIB-1 (Molecular Immunology Borstel-1), is a protein marker used to assess the proliferative activity of cells in various tissues, including cancer cells. Immunohistochemistry (IHC) is a common technique used to detect and quantify Ki-67 expression in tissue samples. Here’s how Ki-67 (MIB-1) testing by IHC typically works:

Sample Collection: A tissue sample, typically obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains cells of interest, such as cancer cells.
Tissue Preparation: The collected tissue sample is processed and prepared for IHC analysis. This involves embedding the tissue in paraffin wax, cutting thin sections (usually around 3-5 micrometers) from the tissue block, and mounting them on glass slides.
IHC Staining: Specific antibodies designed to target the Ki-67 protein are applied to the tissue sections. These antibodies are tagged with a colored or fluorescent label. If Ki-67 protein is present in the cells, the antibodies will bind to it.
Visualization: After the antibodies have been applied and allowed to bind to the Ki-67 protein, the tissue sections are examined under a microscope. The presence of Ki-67 protein is visualized as staining within the cell nuclei.
Quantification: The Ki-67 proliferative index is typically expressed as a percentage. It represents the proportion of cells with positive Ki-67 staining out of the total number of cells in the examined area. This index is an indicator of the proportion of actively dividing cells in the tissue.

Ki-67 (MIB-1) testing is widely used in oncology, especially in the evaluation of cancerous tissues. The Ki-67 proliferative index can provide valuable information about the aggressiveness of tumors and their growth potential. High Ki-67 expression is often associated with more aggressive and rapidly growing tumors, while low Ki-67 expression is associated with slower-growing tumors.

In breast cancer, for example, the Ki-67 proliferative index can help determine the tumor’s subtype and may influence treatment decisions. High Ki-67 levels in breast cancer can indicate a more aggressive phenotype and may be considered when selecting treatment options.

It’s important to note that Ki-67 results should be interpreted in conjunction with other clinical and pathological factors to make informed decisions about cancer diagnosis, prognosis, and treatment. The specific threshold used to classify Ki-67 as high or low can vary depending on the type of cancer and established guidelines. The interpretation of Ki-67 results is typically performed by pathologists who are experienced in cancer diagnostics.

Microsatellite Instability (MSI) by IHC:

Microsatellite instability (MSI) is a condition characterized by the presence of errors or mutations in microsatellite regions of DNA, which are repetitive sequences of DNA bases. MSI can occur in various types of cancer, and it is most commonly associated with colorectal cancer. Immunohistochemistry (IHC) is one of the methods used to assess MSI status in tumor tissues. Here’s how MSI testing by IHC typically works:

Sample Collection: A tissue sample, often obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains tumor cells.
Tissue Preparation: The collected tissue sample is processed and prepared for IHC analysis. Thin sections of the tissue are typically placed on glass slides for further testing.
IHC Staining: Specific antibodies are applied to the tissue sections to detect the presence of proteins associated with DNA mismatch repair (MMR) system. The most commonly tested MMR proteins include MLH1 (MutL homolog 1), MSH2 (MutS homolog 2), MSH6 (MutS homolog 6), and PMS2 (postmeiotic segregation increased 2).
Visualization: After the antibodies have been applied and allowed to bind to the MMR proteins, the tissue sections are examined under a microscope. The presence or absence of staining in the cell nuclei is assessed.
Interpretation: The interpretation of MSI testing by IHC is based on the presence or absence of staining for specific MMR proteins. If there is a lack of staining for one or more of these proteins in tumor cells, it suggests the loss of function or inactivation of the corresponding MMR gene. This loss of MMR protein function can lead to MSI in the tumor tissue.
MSI Classification: Based on the IHC results, tumors are classified as MSI-High (MSI-H), MSI-Low (MSI-L), or Microsatellite Stable (MSS):
- MSI-High (MSI-H): This classification indicates the presence of MSI in the tumor. It means that there is a significant deficiency in one or more MMR proteins.
- MSI-Low (MSI-L): This classification suggests a partial deficiency in MMR protein expression, resulting in a lower degree of MSI compared to MSI-H.
- Microsatellite Stable (MSS): Tumors classified as MSS do not exhibit MSI and have intact MMR protein expression.

MSI testing by IHC is particularly important in the management of colorectal cancer. MSI-High tumors are more likely to respond to certain immunotherapy drugs, such as pembrolizumab, which target immune checkpoints like PD-1. Therefore, knowing the MSI status of a colorectal tumor can guide treatment decisions.

In addition to colorectal cancer, MSI testing by IHC may also be performed in other cancer types, including endometrial cancer and some cases of gastric and ovarian cancers, to assess MSI status and potentially guide treatment decisions. Interpretation of MSI results should be conducted by experienced pathologists who are familiar with the clinical significance of MSI in different cancer types.

PDL-1 (22C3) by IHC:

Programmed Death-Ligand 1 (PD-L1) is a protein expressed on the surface of some cancer cells and other immune cells. PD-L1 plays a key role in regulating the immune response and can interact with its receptor, PD-1, on immune cells to suppress immune activity. Immunohistochemistry (IHC) is a diagnostic technique used to assess the expression of PD-L1 in cancer tissues. Here’s how PD-L1 (22C3) testing by IHC typically works:

Sample Collection: A tissue sample, often obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains tumor cells or cells of interest.
Tissue Preparation: The collected tissue sample is processed and prepared for IHC analysis. Thin sections of the tissue are typically placed on glass slides for further testing.
IHC Staining: Specific antibodies, such as the 22C3 antibody, are applied to the tissue sections to detect the presence and distribution of PD-L1 protein. These antibodies are tagged with a colored or fluorescent label.
Visualization: After the antibodies have been applied and allowed to bind to the PD-L1 protein, the tissue sections are examined under a microscope. The presence or absence of staining in the tumor cells is assessed.
Scoring: The interpretation of PD-L1 testing by IHC involves scoring the staining patterns based on the proportion of tumor cells showing PD-L1 expression and the intensity of staining. Different scoring systems may be used, and the specific criteria can vary depending on the type of cancer and the testing platform used.
- Tumor Proportion Score (TPS): This score represents the percentage of tumor cells showing PD-L1 expression. For example, a TPS of 1% means that 1% of tumor cells express PD-L1.
- Combined Positive Score (CPS): CPS includes the percentage of tumor cells with PD-L1 expression as well as the percentage of immune cells (such as lymphocytes) with PD-L1 expression. This score takes into account both tumor and immune cell PD-L1 expression.

The results of PD-L1 (22C3) testing by IHC are used to classify tumors into different categories:

PD-L1 Positive: Tumors with detectable PD-L1 expression in tumor cells or immune cells based on the specified scoring criteria are considered PD-L1 positive.
PD-L1 Negative: Tumors that do not meet the criteria for PD-L1 positivity are classified as PD-L1 negative.

PD-L1 testing is particularly important in the field of immunotherapy. Some cancer treatments, such as immune checkpoint inhibitors like pembrolizumab (Keytruda), are more likely to be effective in patients with PD-L1-positive tumors. Therefore, knowing the PD-L1 status of a tumor can help guide treatment decisions.

Interpretation of PD-L1 (22C3) results should be conducted by experienced pathologists who are familiar with the specific scoring guidelines and clinical implications of PD-L1 expression in different cancer types. The results are often used in conjunction with other clinical and pathological factors to make informed treatment decisions for cancer patients.

ALK by IHC:

Anaplastic Lymphoma Kinase (ALK) is a gene that can undergo mutations or rearrangements in certain types of cancer, particularly non-small cell lung cancer (NSCLC) and anaplastic large cell lymphoma (ALCL). Immunohistochemistry (IHC) is a diagnostic technique used to assess the expression of the ALK protein in cancer tissues. Here’s how ALK testing by IHC typically works:

Sample Collection: A tissue sample, often obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains cancer cells or cells of interest.
Tissue Preparation: The collected tissue sample is processed and prepared for IHC analysis. Thin sections of the tissue are typically placed on glass slides for further testing.
IHC Staining: Specific antibodies designed to target the ALK protein are applied to the tissue sections. These antibodies are tagged with a colored or fluorescent label.
Visualization: After the antibodies have been applied and allowed to bind to the ALK protein, the tissue sections are examined under a microscope. The presence or absence of staining in the tumor cells is assessed.
Scoring: The interpretation of ALK testing by IHC involves scoring the staining patterns based on the intensity and distribution of staining in tumor cells. Different scoring systems and criteria may be used, depending on the specific test and laboratory protocols.
- Positive Staining: If tumor cells show strong and uniform staining for ALK protein, they are considered ALK-positive.
- Negative Staining: If tumor cells do not show significant staining for ALK protein, they are considered ALK-negative.

ALK testing by IHC is used to identify ALK-positive tumors, which can have important implications for treatment decisions. ALK rearrangements in NSCLC, for example, are associated with sensitivity to ALK inhibitors like crizotinib, alectinib, or ceritinib. These targeted therapies can lead to improved treatment outcomes in patients with ALK-positive NSCLC.

It’s important to note that while ALK testing by IHC is a valuable screening tool, it is not always the definitive method for detecting ALK rearrangements. In cases where ALK IHC results are equivocal or negative but clinical suspicion remains, further testing using techniques like fluorescence in situ hybridization (FISH) or polymerase chain reaction (PCR) may be performed to confirm the presence of ALK rearrangements at the genetic level.

Interpretation of ALK (by IHC) results should be conducted by experienced pathologists who are familiar with the specific criteria and clinical implications of ALK protein expression in different cancer types. The results are often used to guide treatment decisions for cancer patients.

ROS1 by IHC:

ROS1 (c-ros oncogene 1) is a gene that can undergo rearrangements in certain types of cancer, particularly non-small cell lung cancer (NSCLC). Immunohistochemistry (IHC) is a diagnostic technique used to assess the expression of the ROS1 protein in cancer tissues. Here’s how ROS1 testing by IHC typically works:

Sample Collection: A tissue sample, often obtained through a biopsy or surgical procedure, is collected from the patient. This tissue sample contains cancer cells or cells of interest.
Tissue Preparation: The collected tissue sample is processed and prepared for IHC analysis. Thin sections of the tissue are typically placed on glass slides for further testing.
IHC Staining: Specific antibodies designed to target the ROS1 protein are applied to the tissue sections. These antibodies are tagged with a colored or fluorescent label.
Visualization: After the antibodies have been applied and allowed to bind to the ROS1 protein, the tissue sections are examined under a microscope. The presence or absence of staining in the tumor cells is assessed.
Scoring: The interpretation of ROS1 testing by IHC involves scoring the staining patterns based on the intensity and distribution of staining in tumor cells. Different scoring systems and criteria may be used, depending on the specific test and laboratory protocols.
- Positive Staining: If tumor cells show strong and uniform staining for ROS1 protein, they are considered ROS1-positive.
- Negative Staining: If tumor cells do not show significant staining for ROS1 protein, they are considered ROS1-negative.

ROS1 testing by IHC is used to identify ROS1-positive tumors, which can have important implications for treatment decisions. ROS1 rearrangements in NSCLC are associated with sensitivity to ROS1 inhibitors like crizotinib, entrectinib, or ceritinib. These targeted therapies can lead to improved treatment outcomes in patients with ROS1-positive NSCLC.

It’s important to note that while ROS1 testing by IHC is a valuable screening tool, it is not always the definitive method for detecting ROS1 rearrangements. In cases where ROS1 IHC results are equivocal or negative but clinical suspicion remains, further testing using techniques like fluorescence in situ hybridization (FISH) or polymerase chain reaction (PCR) may be performed to confirm the presence of ROS1 rearrangements at the genetic level.

Interpretation of ROS1 (by IHC) results should be conducted by experienced pathologists who are familiar with the specific criteria and clinical implications of ROS1 protein expression in different cancer types. The results are often used to guide treatment decisions for cancer patients.

ER,PR, Her2-neu:

ER (Estrogen Receptor), PR (Progesterone Receptor), and HER2-neu (Human Epidermal Growth Factor Receptor 2) are biomarkers frequently assessed in breast cancer to guide diagnosis and treatment decisions:

ER (Estrogen Receptor): ER is a protein found on the surface of breast cancer cells. Its presence or absence indicates whether the cancer is sensitive to estrogen, a hormone that can promote cancer cell growth. Breast cancers that are ER-positive can often be treated with hormone therapy, such as tamoxifen or aromatase inhibitors, to block the effects of estrogen and slow down cancer growth.

- ER-Positive (ER+): Indicates the presence of estrogen receptors in cancer cells.
- ER-Negative (ER-): Indicates the absence of estrogen receptors.

PR (Progesterone Receptor): Similar to ER, PR is a protein found on the surface of breast cancer cells. Its presence or absence is another indicator of hormone sensitivity. PR status is often evaluated along with ER status to guide hormone therapy decisions.

- PR-Positive (PR+): Indicates the presence of progesterone receptors in cancer cells.
- PR-Negative (PR-): Indicates the absence of progesterone receptors.

HER2-neu (Human Epidermal Growth Factor Receptor 2): HER2-neu is a protein receptor involved in cell growth and division. In some breast cancers, the HER2 gene is amplified, leading to overexpression of HER2 protein. HER2-positive breast cancer tends to be more aggressive, but it can be targeted with drugs like trastuzumab (Herceptin) and other HER2-targeted therapies.

- HER2-Positive (HER2+): Indicates the overexpression or amplification of HER2-neu in cancer cells.
- HER2-Negative (HER2-): Indicates normal levels of HER2-neu.

The results of ER, PR, and HER2-neu testing are used to classify breast cancer into different subtypes, which can guide treatment decisions. For example:

Hormone receptor-positive (ER+ and/or PR+) breast cancer may benefit from hormone therapy.
HER2-positive breast cancer may be treated with HER2-targeted therapies in addition to standard treatments.
Triple-negative breast cancer lacks expression of ER, PR, and HER2-neu and may be treated differently, often with chemotherapy.

These biomarker tests help oncologists tailor treatment plans to the specific characteristics of each patient’s breast cancer. Additionally, they provide important information about prognosis and can help predict how the cancer is likely to respond to certain treatments. Interpretation of these results is typically performed by pathologists or oncologists, and they play a significant role in personalized cancer care.

NIPT:

NIPT stands for Non-Invasive Prenatal Testing. It is a relatively new and advanced screening method used during pregnancy to assess the risk of certain genetic conditions in the fetus. NIPT is typically performed early in pregnancy, typically between 10 and 13 weeks gestation, although it can be done later as well. Here’s how NIPT works and what it can detect:

Non-Invasive: NIPT is non-invasive, which means it doesn’t require any invasive procedures like amniocentesis or chorionic villus sampling (CVS). Instead, it relies on a simple blood draw from the pregnant person.
Fetal DNA: During pregnancy, a small amount of the fetal DNA (cell-free fetal DNA or cfDNA) from the developing placenta circulates in the pregnant person’s bloodstream. NIPT analyzes this fetal DNA to look for genetic abnormalities.
Genetic Conditions Detected: NIPT primarily screens for the following genetic conditions:

Trisomy 21 (Down syndrome): Caused by an extra chromosome 21, individuals with Down syndrome typically have cognitive and physical developmental delays.
Trisomy 18 (Edwards syndrome): Caused by an extra chromosome 18, Edwards syndrome leads to severe developmental and health problems.
Trisomy 13 (Patau syndrome): Caused by an extra chromosome 13, Patau syndrome results in severe intellectual and physical disabilities.
Sex Chromosome Aneuploidies: NIPT can also detect conditions related to sex chromosome abnormalities, such as Turner syndrome (monosomy X), Klinefelter syndrome (XXY), and others.

Sex Determination: NIPT can also reveal the baby’s sex early in pregnancy, which some parents find interesting or helpful in preparing for the birth.
Accuracy: NIPT is highly accurate, especially for detecting Down syndrome. It has a lower false-positive rate compared to traditional prenatal screening methods like maternal serum screening.
Limited Scope: NIPT is a screening test, not a diagnostic test. This means that while it can provide a high level of accuracy, a positive result should be followed by diagnostic testing (like amniocentesis or CVS) to confirm the presence of a genetic condition.

It’s important to note that NIPT is typically offered to pregnant individuals who have an increased risk of carrying a baby with a genetic condition, such as those with advanced maternal age or those with a family history of genetic disorders. Some healthcare providers may offer NIPT as a routine screening option for all pregnant individuals.

NIPT is a valuable tool for prenatal care, as it provides early and accurate information about the fetus’s genetic health without posing the same risks as invasive procedures. However, it’s important to discuss the test with a healthcare provider to determine whether it’s appropriate for a specific pregnancy and to understand its limitations.

NIPT with Micro Deletions:

Non-Invasive Prenatal Testing (NIPT) with Micro Deletions refers to an extended version of standard NIPT that includes screening for specific microdeletion syndromes in addition to the common trisomies (like Down syndrome, Edwards syndrome, and Patau syndrome) and sex chromosome abnormalities. Microdeletion syndromes are rare genetic conditions caused by the deletion of a small segment of a chromosome. NIPT with microdeletion screening can provide information about the risk of these rare conditions in a developing fetus.

Some of the microdeletion syndromes that may be included in NIPT with microdeletion screening are:

22q11.2 Deletion Syndrome (DiGeorge Syndrome or VCFS): This syndrome results from the deletion of a small piece of chromosome 22 and can lead to a wide range of developmental and health issues, including heart defects, immune system problems, and learning disabilities.
1p36 Deletion Syndrome: Caused by a deletion on the short arm of chromosome 1, this syndrome is associated with developmental delays, intellectual disabilities, and distinctive facial features.
Cri-du-chat Syndrome: This condition is caused by a deletion on the short arm of chromosome 5 and is characterized by a distinctive cry (resembling a cat’s cry), intellectual disabilities, and developmental delays.
Prader-Willi Syndrome: This syndrome is caused by the loss of specific genes on chromosome 15. It leads to developmental and intellectual challenges, as well as hyperphagia (an insatiable appetite).
Angelman Syndrome: Also caused by the loss of specific genes on chromosome 15, Angelman syndrome results in developmental delays, speech impairments, and a happy and excitable demeanor.

NIPT with microdeletion screening analyzes cell-free fetal DNA in the pregnant person’s blood to detect the presence of specific microdeletion syndromes. However, it’s important to understand the following:

These tests are screening tests, not diagnostic tests. A positive result indicates an increased risk but does not confirm the presence of the microdeletion syndrome in the fetus.
If a positive result is obtained, further diagnostic testing, such as chorionic villus sampling (CVS) or amniocentesis, is typically recommended to confirm the diagnosis.
The accuracy of NIPT with microdeletion screening varies depending on the syndrome being tested. It is generally more accurate for detecting some microdeletion syndromes than others.
Not all NIPT tests include microdeletion screening. It’s important to discuss the specific test options and their coverage with a healthcare provider.

NIPT with microdeletion screening can provide valuable information about the risk of rare genetic conditions in the developing fetus, but it should be used in conjunction with genetic counseling and, if necessary, confirmatory diagnostic testing. Healthcare providers can help individuals and couples make informed decisions about whether to undergo this type of screening during pregnancy.

BRCA 1&2 Deletion & Duplication:

BRCA1 and BRCA2 are human genes that produce proteins that help suppress the growth of tumors. Mutations in these genes can increase the risk of certain cancers, particularly breast and ovarian cancer. Deletions and duplications in the BRCA1 and BRCA2 genes are types of genetic mutations that can be associated with increased cancer risk.

BRCA1 and BRCA2 Deletion: A deletion mutation in the BRCA1 or BRCA2 gene involves the loss or deletion of a section of the gene’s DNA sequence. These deletions can lead to the loss of normal gene function, making the individual more susceptible to cancer.
BRCA1 and BRCA2 Duplication: A duplication mutation in the BRCA1 or BRCA2 gene involves the presence of extra copies or duplicates of certain segments of the gene’s DNA sequence. Duplication mutations can also disrupt the normal function of the gene and increase cancer risk.

Individuals with BRCA1 or BRCA2 mutations, including deletions or duplications, have an elevated risk of developing breast, ovarian, and certain other cancers. These mutations can be inherited from one’s parents or occur spontaneously in a person’s DNA. They are considered to be hereditary cancer susceptibility genes.

To determine whether an individual has a BRCA1 or BRCA2 deletion or duplication, genetic testing can be performed. This testing involves analyzing a person’s DNA to identify mutations in these genes. The process typically includes the following steps:

DNA Sample Collection: A blood sample or saliva sample is collected from the individual.
DNA Sequencing: The DNA sample is analyzed to determine the sequence of the BRCA1 and BRCA2 genes.
Copy Number Analysis: In addition to sequencing, copy number analysis is performed to identify deletions or duplications within the genes. This analysis can detect changes in the number of copies of specific gene segments.
Interpretation: The results of the genetic testing are interpreted to identify any mutations, including deletions or duplications, in the BRCA1 and BRCA2 genes.
Genetic Counseling: Individuals who test positive for BRCA1 or BRCA2 mutations, including deletions or duplications, are typically referred for genetic counseling. Genetic counselors can provide information about cancer risk, prevention strategies, and potential medical interventions.
Medical Management: Depending on the test results and the individual’s family history, healthcare providers may recommend personalized cancer risk reduction strategies, such as increased surveillance, preventive surgeries, or chemoprevention.

BRCA1 and BRCA2 genetic testing, including analysis for deletions and duplications, can provide important information for individuals and families at risk of hereditary breast and ovarian cancer. It allows for informed decisions about cancer risk management and prevention strategies. Genetic counseling is an essential component of this process to help individuals understand their risk and make informed choices.

Somatic Panel- 50 Gene:

A somatic panel of 50 genes refers to a genetic testing panel that analyzes specific genetic mutations in the DNA of somatic (non-germline) cells. These types of panels are typically used in the context of cancer diagnostics and treatment planning. Here’s what you need to know:

Somatic vs. Germline Mutations: Somatic mutations are genetic changes that occur in a person’s body cells (somatic cells) other than the germ cells (sperm and egg cells). These mutations are not passed on to offspring and are not present in every cell of the body. In contrast, germline mutations are inherited and are present in all cells, including sperm and egg cells.
Cancer and Somatic Mutations: Cancer is often driven by the accumulation of somatic mutations in specific genes. These mutations can lead to uncontrolled cell growth and the development of tumors. Identifying these somatic mutations is crucial for understanding the genetic basis of a person’s cancer and for tailoring cancer treatments.
Somatic Panel of 50 Genes: A somatic panel of 50 genes is a genetic testing panel that examines a specific set of 50 genes known to be associated with various cancer types. These genes are often implicated in tumor development and progression. By analyzing the genetic makeup of a tumor, healthcare providers can gain insights into the specific genetic mutations driving the cancer.
Targeted Therapies: Identifying somatic mutations through genetic testing allows oncologists to select targeted therapies that are designed to inhibit the effects of these specific mutations. Targeted therapies are often more precise and have fewer side effects compared to traditional chemotherapy.
Personalized Treatment: Somatic panel testing is part of personalized or precision medicine. It helps guide treatment decisions by matching the genetic profile of the tumor with therapies that are most likely to be effective.
Tumor Types: Somatic panel testing can be used for various cancer types, including lung cancer, breast cancer, colorectal cancer, melanoma, and many others. The choice of genes included in the panel may vary depending on the specific cancer type and the laboratory performing the testing.
Interpretation: The results of somatic panel testing are interpreted by oncologists and geneticists to identify specific mutations in the tumor. The interpretation takes into account the clinical relevance of these mutations and informs treatment decisions.

Somatic panel testing has become an important tool in cancer care, enabling more precise and individualized approaches to treatment. By understanding the genetic alterations driving a patient’s cancer, healthcare providers can select therapies that are more likely to be effective, potentially leading to better outcomes and fewer side effects. It’s important for individuals with cancer to discuss the possibility of genetic testing with their healthcare team to determine if it’s appropriate for their specific situation.

Somatic Panel- 161 Gene- POLE & NTRK:

A somatic panel of 161 genes, including genes such as POLE and NTRK, refers to an extended genetic testing panel that analyzes specific genetic mutations in the DNA of somatic (non-germline) cells. These panels are typically used in the context of cancer diagnostics and treatment planning and are part of the broader field of precision medicine. Here’s some information about these genes and their significance:

POLE Gene: The POLE (DNA polymerase epsilon, catalytic subunit) gene is involved in DNA replication and repair. Mutations in the POLE gene can lead to a high mutation rate in cancer cells, which is sometimes referred to as “ultramutated” or “hypermutated” tumors. POLE mutations are most commonly associated with endometrial (uterine) cancer but can occur in other cancer types as well. Identifying a POLE mutation can have implications for treatment decisions and prognosis.
NTRK Genes: The NTRK (Neurotrophic Tyrosine Receptor Kinase) genes, including NTRK1, NTRK2, and NTRK3, code for receptor proteins that play a role in cell growth and differentiation. NTRK gene fusions, which result from genetic rearrangements, can lead to the development of certain types of cancer, including some rare forms of pediatric cancers and some adult cancers like solid tumors. Detection of NTRK fusions can be important for selecting targeted therapies, such as larotrectinib and entrectinib, which specifically inhibit the NTRK fusion proteins.

A somatic panel of 161 genes goes beyond the analysis of common cancer-related genes and includes a broader set of genes associated with various cancer types. These panels are designed to identify specific genetic alterations, such as point mutations, insertions, deletions, and gene fusions, that drive cancer growth. By characterizing the genetic makeup of a tumor through such panels, oncologists can make more informed decisions about treatment options.

Key points about somatic panel testing with a focus on genes like POLE and NTRK:

It provides information about specific genetic mutations in the tumor cells.
It helps guide treatment decisions, particularly when targeted therapies are available.
It may be used in various cancer types to identify rare or less common genetic alterations.
The interpretation of somatic panel results is typically performed by oncologists and geneticists to determine the clinical relevance of identified mutations.

Patients with cancer who are being considered for targeted therapies or have specific clinical indications may undergo somatic panel testing to better understand the genetic characteristics of their tumors. It’s important to discuss the potential benefits and limitations of such testing with healthcare providers to determine if it’s appropriate for a particular case.

Somatic Panel for CA Endometrium:

A somatic panel for endometrial cancer (also known as uterine cancer) is a genetic testing panel that analyzes specific genetic mutations in the DNA of somatic (non-germline) cells from endometrial tumors. This type of genetic testing is used to characterize the genetic makeup of the tumor, identify specific genetic alterations, and guide treatment decisions. Here’s what you need to know about somatic panels for endometrial cancer:

Endometrial Cancer: Endometrial cancer originates in the lining of the uterus (the endometrium). It is one of the most common gynecological cancers. The genetic characteristics of the tumor can vary from one patient to another, influencing its behavior and response to treatment.
Somatic Panel Testing: A somatic panel for endometrial cancer typically includes a set of genes associated with this specific cancer type. These genes may be mutated or altered in endometrial tumors and can drive tumor growth. The panel may include genes related to DNA repair, cell cycle regulation, and other cellular processes involved in cancer development.
Common Genetic Alterations: Some of the common genetic alterations in endometrial cancer include mutations in genes such as PTEN, TP53, KRAS, PIK3CA, and CTNNB1 (beta-catenin). These mutations can provide insights into the aggressiveness of the tumor and its potential response to targeted therapies.
Personalized Treatment: The results of somatic panel testing help oncologists make personalized treatment decisions. For example, if a specific genetic alteration is detected, a targeted therapy that matches that alteration may be considered as part of the treatment plan.
Prognostic Information: In addition to guiding treatment decisions, somatic panel testing can also provide valuable prognostic information. Certain genetic alterations may be associated with a more favorable or unfavorable prognosis.
Clinical Trials: Somatic panel testing can identify patients who may be eligible for clinical trials investigating novel therapies, including targeted therapies or immunotherapies.
Interpretation: The interpretation of somatic panel results is typically performed by oncologists, geneticists, or molecular pathologists who are experienced in cancer genetics. They assess the clinical relevance of identified genetic alterations and their implications for treatment and prognosis.

It’s important to note that somatic panel testing for endometrial cancer is not always part of standard practice but may be recommended in specific clinical scenarios, such as advanced or recurrent disease. The decision to undergo somatic panel testing should be discussed with healthcare providers, taking into account the individual patient’s medical history, stage of the disease, and treatment goals.

Somatic panel testing is part of the broader field of precision medicine, which aims to tailor cancer treatment to the genetic characteristics of the tumor. By identifying key genetic alterations, oncologists can optimize treatment strategies to improve outcomes and minimize side effects.

Somatic Panel Comprehensive genomic profiling with TMB, MSI, DNA and RNA- 590 Genes:

Comprehensive genomic profiling (CGP) with TMB (Tumor Mutational Burden), MSI (Microsatellite Instability), DNA, and RNA analysis involving 590 genes is an advanced genetic testing approach used in cancer research and clinical practice. This testing methodology is designed to provide a comprehensive understanding of the genetic alterations within a tumor, which can have important implications for cancer diagnosis, prognosis, and treatment planning. Here’s a breakdown of the key components of this testing:

Comprehensive Genomic Profiling (CGP): CGP involves analyzing the DNA and RNA of tumor cells to identify a wide range of genetic alterations, including mutations, amplifications, deletions, translocations, and other genomic changes. It assesses multiple genes simultaneously, allowing for a comprehensive view of the tumor’s genetic landscape.
Tumor Mutational Burden (TMB): TMB is a measure of the total number of mutations present in the DNA of tumor cells. High TMB can indicate an increased likelihood of response to immunotherapy, as tumors with a high mutational burden are more likely to generate neoantigens that can be recognized by the immune system.
Microsatellite Instability (MSI): MSI testing assesses the stability of microsatellite regions in the tumor’s DNA. MSI-high tumors have a high degree of instability, which can be indicative of a deficiency in DNA repair mechanisms. MSI-high status is important in cancer diagnosis and may influence treatment decisions, particularly in colorectal and other cancers.
DNA Analysis: DNA analysis involves examining the genetic code of tumor cells to identify mutations, copy number alterations, and structural variations within specific genes. This information can help determine targeted therapies, predict drug resistance, and provide insights into cancer biology.
RNA Analysis: RNA analysis focuses on the expression of genes in tumor cells. It measures the levels of messenger RNA (mRNA) produced by genes and can provide insights into the activity of specific genes, pathways, and potential drug targets.
590 Genes: The use of a panel that includes 590 genes allows for a comprehensive assessment of genetic alterations. These genes may include those known to be associated with various cancer types, as well as genes involved in key cellular processes, signaling pathways, and DNA repair mechanisms.
Clinical Implications: The results of comprehensive genomic profiling with TMB, MSI, DNA, and RNA analysis can have significant clinical implications. They can guide treatment decisions by identifying targetable mutations, predicting immunotherapy response, and helping oncologists select appropriate therapies.

This level of comprehensive genetic testing is particularly valuable in the era of precision medicine, where treatment decisions are increasingly based on the genetic characteristics of the tumor. It allows oncologists to tailor treatment plans to individual patients and their specific cancer profiles. However, it’s important to note that not all patients with cancer may require such extensive testing, and the decision to undergo CGP should be made in consultation with healthcare providers based on the clinical context and specific tumor characteristics.

Tumor Mutation Burden (TMB):

Tumor Mutation Burden (TMB) is a measure of the number of genetic mutations or alterations present in the DNA of tumor cells within a specific tumor sample. It is an important biomarker used in cancer research and clinical practice to assess the overall mutational load of a tumor. Here are key points about TMB:

Definition: TMB quantifies the total number of somatic mutations, including point mutations (single nucleotide changes) and other types of genetic alterations (such as insertions and deletions), found within the coding regions of a tumor’s DNA. It is typically reported as the number of mutations per megabase (Mb) of DNA.
High vs. Low TMB: TMB is categorized as either high or low based on a specific threshold value. The threshold for defining high TMB may vary in different contexts and clinical studies. Generally, a higher number of mutations per megabase indicates high TMB, while a lower number indicates low TMB.
Immunotherapy Response: TMB is associated with the likelihood of a positive response to immunotherapy, particularly immune checkpoint inhibitors like anti-PD-1 and anti-PD-L1 antibodies. High TMB is often correlated with a more favorable response to immunotherapy because tumors with a high mutational burden tend to produce more neoantigens (new antigens) that can be recognized by the immune system.
Immune Recognition: High TMB tumors are more likely to trigger an immune response, as the greater number of mutations leads to the production of abnormal proteins (neoantigens) that immune cells can detect. This can enhance the effectiveness of immunotherapy by boosting the body’s ability to target and attack the tumor.
Tumor Types: TMB can vary widely between different cancer types and even within subtypes of the same cancer. Some cancer types, such as melanoma and lung cancer (particularly non-small cell lung cancer), are more likely to have high TMB.
Clinical Use: TMB assessment is increasingly used in clinical practice to guide treatment decisions. Patients with high TMB may be considered candidates for immunotherapy, while those with low TMB may be more likely to benefit from other treatment options like targeted therapies or chemotherapy.
Testing Methods: TMB can be determined through next-generation sequencing (NGS) or whole exome sequencing (WES) of the tumor’s DNA. These methods identify and count mutations within coding regions.
Limitations: While TMB is a valuable biomarker, it is not the sole predictor of immunotherapy response. Other factors, such as the specific immune microenvironment of the tumor, the presence of certain genetic alterations (e.g., microsatellite instability or MSI), and individual patient characteristics, also play a role in determining treatment outcomes.

In summary, Tumor Mutation Burden is a measure of genetic mutations within a tumor and is used to predict the likelihood of a positive response to immunotherapy. It is an important tool in personalized cancer treatment, helping oncologists make informed decisions about treatment options for their patients.

BRCA 1 & 2 Somatic Panel:

BRCA1 and BRCA2 somatic mutations refer to genetic alterations in the BRCA1 and BRCA2 genes that occur specifically within the cancer cells of an individual, as opposed to being inherited. These mutations can contribute to the development and progression of certain types of cancer. Here’s a closer look at somatic mutations in BRCA1 and BRCA2:

Somatic Mutations: Somatic mutations are genetic changes that occur within the DNA of an individual’s body cells, including cancer cells, during their lifetime. These mutations are not present in the germline (sperm or egg cells) and are not inherited but are rather acquired as a result of various factors, such as exposure to environmental carcinogens or errors in DNA replication.
BRCA1 and BRCA2 Genes: BRCA1 and BRCA2 are tumor suppressor genes that play a crucial role in repairing damaged DNA and maintaining genomic stability. When somatic mutations occur in these genes within cancer cells, they can disrupt the normal functioning of BRCA1 and BRCA2.
Deficient DNA Repair: Somatic mutations in BRCA1 or BRCA2 can lead to deficiencies in the DNA repair mechanisms in cancer cells. This deficiency can result in the accumulation of genetic alterations and genomic instability, increasing the risk of further mutations and potentially contributing to cancer progression.
Association with Cancer: Somatic mutations in BRCA1 and BRCA2 are particularly relevant in breast and ovarian cancers. These mutations can increase the risk of developing these cancers and may also have implications for treatment decisions.
Treatment Implications: The presence of somatic mutations in BRCA1 or BRCA2 can impact treatment options. Cancer cells with these mutations may respond differently to certain therapies. For instance, tumors with BRCA1 or BRCA2 mutations may be more sensitive to treatments like platinum-based chemotherapy or PARP (Poly ADP-ribose polymerase) inhibitors. PARP inhibitors have shown effectiveness in treating cancers with BRCA1/2 mutations by exploiting the DNA repair deficiency in these cells.
Somatic Mutation Testing: Detecting somatic mutations in BRCA1 and BRCA2 usually requires specialized genetic testing of the tumor tissue. This is distinct from germline mutation testing, which is conducted on DNA obtained from blood or saliva samples. Somatic mutation testing is typically performed on the cancer tissue obtained through biopsy or surgery.
Clinical Significance: The clinical significance of somatic BRCA1 and BRCA2 mutations can vary based on the specific genetic alterations and cancer type. Oncologists consider these mutations when making treatment decisions and may opt for therapies that target the DNA repair deficiencies associated with these mutations.

In summary, somatic mutations in BRCA1 and BRCA2 can occur within cancer cells and may influence cancer development and response to treatment. Identifying these mutations through specialized testing can have clinical implications, potentially guiding treatment choices and leading to more tailored cancer therapies.

Leukemia Panel NGS- 40 Genes and 29 fusions (DNA and RNA):

A leukemia panel using next-generation sequencing (NGS) that analyzes 40 genes and 29 fusions involving both DNA and RNA is a comprehensive genetic testing approach used in the diagnosis, classification, and personalized treatment of leukemia. Leukemia is a type of blood cancer characterized by the abnormal proliferation of white blood cells. Here’s what you need to know about this type of genetic testing:

NGS Technology: Next-generation sequencing (NGS) is a high-throughput genetic sequencing method that allows for the simultaneous analysis of multiple genes and genetic alterations in a single test. It is a powerful tool for understanding the genetic basis of cancer.
Leukemia Panel: A leukemia panel typically includes a selection of genes known to be associated with various forms of leukemia. These genes may include oncogenes (genes that promote cancer growth) and tumor suppressor genes (genes that inhibit cancer growth).
Genetic Alterations: The panel assesses a wide range of genetic alterations, including point mutations, insertions, deletions, and gene fusions. These alterations can play a crucial role in the development and progression of leukemia.
Fusion Genes: Fusion genes are created when two different genes fuse together, often as a result of chromosomal rearrangements. These fusion events can lead to the production of abnormal proteins that drive leukemia. The testing of RNA can help detect these fusion events.
Classification and Subtyping: Genetic testing of leukemia helps classify and subtype the disease. Leukemia is not a single disease but a group of diseases with diverse genetic profiles. Identifying specific genetic alterations can help clinicians determine the type of leukemia a patient has.
Personalized Treatment: The results of the leukemia panel can guide treatment decisions. Certain genetic alterations may make leukemia cells more susceptible to specific targeted therapies, while others may indicate a need for traditional chemotherapy or stem cell transplantation.
Monitoring: In addition to diagnosis and treatment planning, genetic testing can be used for disease monitoring and to detect minimal residual disease (MRD), which refers to the presence of a small number of leukemia cells that remain after treatment.
Clinical Trials: Genetic testing results may also make patients eligible for clinical trials exploring novel treatments based on specific genetic alterations.
Prognosis: Some genetic alterations can provide information about prognosis and the likelihood of treatment response or relapse.

In summary, a leukemia panel using NGS technology that analyzes 40 genes and 29 fusions involving both DNA and RNA is a valuable tool in the management of leukemia. It helps clinicians make precise diagnoses, classify the disease, and select the most appropriate treatment strategies based on the genetic characteristics of the leukemia. This approach contributes to the advancement of personalized medicine in leukemia care, ultimately improving patient outcomes.

Liquid Biopsy (ctDNA)- 50 genes:

A liquid biopsy, specifically focused on circulating tumor DNA (ctDNA) analysis, targeting 50 genes, is a type of non-invasive genetic testing used in cancer diagnosis and monitoring. This approach involves the detection and analysis of small fragments of DNA released by cancer cells into the bloodstream. Here’s what you need to know about a liquid biopsy targeting 50 genes:

Liquid Biopsy: Unlike traditional biopsies, which involve the removal of tissue samples from a tumor, liquid biopsies are minimally invasive and rely on a simple blood draw. They are particularly useful for assessing the genetic makeup of tumors in a less invasive manner.
ctDNA: Circulating tumor DNA (ctDNA) refers to small fragments of DNA shed into the bloodstream by cancer cells. These fragments can carry genetic mutations and other alterations that are characteristic of the tumor.
Analysis of 50 Genes: Liquid biopsy panels targeting 50 genes are designed to provide a broad and comprehensive view of genetic alterations in cancer. These genes are often associated with various cancer types and may include oncogenes, tumor suppressor genes, and genes related to DNA repair and cellular signaling pathways.
Cancer Diagnosis: Liquid biopsies can be used to aid in the diagnosis of cancer, particularly when it is challenging to obtain tissue samples for a traditional biopsy. By identifying specific genetic mutations in ctDNA, clinicians can confirm the presence of cancer and classify its type.
Treatment Selection: Genetic testing of ctDNA can guide treatment decisions by identifying targetable mutations or alterations. It can help oncologists select therapies, including targeted therapies and immunotherapies, that are more likely to be effective against the specific genetic profile of the tumor.
Monitoring Treatment Response: Liquid biopsies are valuable for monitoring the response to cancer treatment over time. Changes in ctDNA levels or the presence of new mutations can indicate treatment efficacy or disease progression.
Minimal Residual Disease (MRD): Liquid biopsies can also detect minimal residual disease (MRD), which refers to the presence of a small number of cancer cells that remain in the body after treatment. Monitoring MRD can help assess the risk of recurrence.
Prognostic Information: Information obtained from ctDNA analysis can provide insights into the prognosis of cancer, helping to predict the likelihood of disease recurrence and patient outcomes.
Research and Clinical Trials: Liquid biopsies are valuable tools in cancer research and may also identify patients who are eligible for specific clinical trials based on their genetic profiles.

In summary, a liquid biopsy targeting 50 genes in ctDNA is a powerful tool for the diagnosis, treatment selection, and monitoring of cancer. It offers a less invasive alternative to traditional biopsies and provides valuable genetic information that can guide personalized cancer care.

Hereditary Cancer Gene Panel:

A hereditary cancer gene panel is a type of genetic testing that analyzes a specific set of genes associated with an increased risk of hereditary or familial cancers. These panels are designed to identify germline (inherited) mutations or genetic variants that can predispose individuals to various types of cancer. Here’s what you need to know about hereditary cancer gene panels:

Genes Included: Hereditary cancer gene panels typically include a group of genes that have been linked to an elevated risk of certain types of cancer. The genes included in these panels can vary depending on the specific panel and the laboratory offering the test. Common genes included in hereditary cancer panels may involve BRCA1 and BRCA2 (associated with breast and ovarian cancer), TP53 (associated with Li-Fraumeni syndrome), MLH1, MSH2, MSH6, PMS2 (associated with Lynch syndrome and colorectal cancer), and others.
Risk Assessment: Genetic testing through a hereditary cancer gene panel helps individuals and their healthcare providers assess the risk of developing specific types of cancer based on their genetic profile. Identifying germline mutations in cancer susceptibility genes can guide personalized cancer risk management and screening strategies.
Inherited Mutations: The mutations detected by these panels are germline mutations, meaning they are inherited from one’s parents and can be passed on to future generations. When present in these genes, mutations increase the likelihood of developing cancer over a person’s lifetime.
Cancer Types: Different genes within the panel are associated with different cancer types. For example, BRCA1 and BRCA2 mutations are linked to breast and ovarian cancer risk, while mutations in genes like APC are associated with colorectal cancer risk. The panel may also include genes associated with other cancer types, such as pancreatic, prostate, or melanoma.
Clinical Implications: Identifying a hereditary cancer risk through genetic testing can have significant clinical implications. It allows for personalized risk management, early detection strategies (such as increased screening or prophylactic surgeries), and informed decisions about cancer prevention and treatment options.
Genetic Counseling: Before undergoing hereditary cancer gene panel testing, individuals are often encouraged to seek genetic counseling. Genetic counselors provide information about the testing process, potential outcomes, and the psychological and familial implications of the results.
Insurance and Privacy: It’s essential to be aware that genetic testing may have implications for insurance coverage and privacy. Some individuals may choose to undergo testing anonymously to protect their privacy.
Family Implications: A positive result can also have implications for family members who may share the same genetic risk. It may lead to cascade testing within families to identify other at-risk individuals.

In summary, hereditary cancer gene panels are valuable tools for identifying inherited genetic mutations associated with an increased risk of cancer. These panels help individuals and their healthcare providers make informed decisions about cancer risk management, prevention, and early detection strategies. Genetic counseling is typically recommended to ensure individuals receive comprehensive information and support throughout the testing process.

Mutation Specific Gene Test:

A mutation-specific gene test, also known as a single-gene mutation test or targeted mutation analysis, is a type of genetic testing that focuses on identifying a specific mutation within a particular gene of interest. Unlike broader genetic tests that analyze multiple genes or an individual’s entire exome or genome, mutation-specific tests are designed to detect a known or suspected mutation in a specific gene. Here’s how mutation-specific gene tests work and their common applications:

Gene of Interest: Mutation-specific gene tests are typically used when there is a specific gene of interest that is associated with a particular condition or disease. This gene may be known to carry specific mutations that are responsible for the disease or condition.
Known Mutation: In many cases, mutation-specific gene tests are used to confirm the presence of a known mutation within the gene. These known mutations may be associated with genetic disorders, hereditary conditions, or specific types of cancer.
Diagnostic Testing: Mutation-specific gene tests are commonly used for diagnostic purposes when a healthcare provider suspects a particular genetic mutation based on clinical symptoms or family history. These tests can confirm or rule out the presence of the suspected mutation.
Carrier Testing: Some mutation-specific tests are used to determine if an individual carries a specific genetic mutation associated with an autosomal recessive disorder. Carriers do not typically display symptoms of the disorder but can pass the mutation on to their offspring.
Prenatal Testing: Mutation-specific gene tests can also be performed during prenatal testing to determine if a fetus has inherited a known disease-causing mutation. This is often done when there is a family history of a genetic disorder.
Cancer Testing: In oncology, mutation-specific gene tests are used to identify specific mutations in cancer-related genes. For example, tests can be performed to detect mutations in genes like EGFR (epidermal growth factor receptor) in lung cancer or BRAF in melanoma.
Treatment Selection: In cancer care, mutation-specific gene tests are crucial for selecting targeted therapies. Identifying specific mutations helps oncologists choose treatments that are more likely to be effective against the cancer’s genetic profile.
Research: Mutation-specific gene tests are also used in genetic research to study the effects of specific mutations on health and disease.
Genetic Counseling: Before and after mutation-specific gene testing, genetic counseling is often recommended to help individuals understand the implications of the results, make informed decisions, and receive support.

It’s important to note that mutation-specific gene tests are only useful when there is a specific genetic mutation suspected or known to be associated with a particular condition or disease. For broader assessments of multiple genes or comprehensive genomic profiling, other types of genetic tests, such as whole exome sequencing or targeted gene panels, may be more appropriate. The choice of genetic testing method depends on the clinical context and the specific genetic question being addressed.

HRR Gene Panel:

The HRR (Homologous Recombination Repair) gene panel is a genetic testing panel that focuses on analyzing a set of genes associated with the homologous recombination repair pathway. The homologous recombination repair pathway is a critical DNA repair mechanism responsible for fixing double-strand DNA breaks and maintaining genomic stability. Mutations or alterations in genes within this pathway can lead to an increased risk of cancer, particularly breast and ovarian cancer. Here’s what you need to know about the HRR gene panel:

Gene Selection: The HRR gene panel typically includes a selection of genes that are involved in the homologous recombination repair pathway. Some of the key genes in this pathway include BRCA1, BRCA2, PALB2, RAD51C, and RAD51D, among others.
DNA Repair Mechanism: Homologous recombination repair is a highly precise DNA repair mechanism that helps correct DNA damage, especially double-strand breaks. Mutations in HRR pathway genes can impair this repair process, leading to genomic instability and an increased susceptibility to cancer.
Cancer Risk Assessment: The HRR gene panel is used to assess an individual’s genetic risk of developing cancer, particularly breast and ovarian cancer. Mutations in genes like BRCA1 and BRCA2 are well-known to increase the risk of these cancers, and they are often included in HRR panels.
Inherited Mutations: Mutations in HRR pathway genes that are detected through this panel are typically germline mutations, meaning they are inherited from one’s parents and can be passed on to future generations. These mutations confer an increased lifetime risk of cancer.
Hereditary Cancer Syndromes: Individuals with mutations in HRR genes are often at risk of hereditary breast and ovarian cancer syndrome (HBOC) or other hereditary cancer syndromes associated with increased cancer risk.
Risk Management: Identifying mutations in HRR genes can guide risk management strategies. This may include increased surveillance, preventive measures, or risk-reducing surgeries.
Treatment Implications: For individuals with cancer, the presence of HRR gene mutations can have implications for treatment. Some targeted therapies and treatments may be more effective for individuals with certain mutations.
Genetic Counseling: Genetic counseling is typically recommended before and after HRR gene panel testing. It helps individuals understand the implications of their genetic results, make informed decisions about cancer risk management, and address emotional and familial concerns.
Research and Clinical Trials: Mutation data from HRR gene panel testing can also contribute to genetic research and may identify individuals who are eligible for specific clinical trials based on their genetic profiles.

In summary, the HRR gene panel is a valuable tool for assessing an individual’s genetic risk of developing cancer, particularly breast and ovarian cancer. It provides essential information that can guide personalized cancer risk management, screening, and treatment strategies. Genetic counseling is often an integral part of the testing process to ensure individuals receive comprehensive support and information.

HRR Gene Panel:

The HRD (Homologous Recombination Deficiency) score is a numerical value that quantifies the extent of defects or deficiencies in the homologous recombination DNA repair pathway within cancer cells. The HRD score is used in oncology to assess the likelihood that a cancer will respond to certain treatments, particularly therapies that exploit DNA repair deficiencies.

Here are some key points about the HRD score:

Homologous Recombination Repair (HRR) Pathway: The HRR pathway is a critical mechanism that cells use to repair double-strand DNA breaks and maintain genomic stability. When this pathway is deficient or defective, it can lead to genomic instability, accumulation of DNA damage, and an increased susceptibility to cancer.
DNA Repair Deficiency in Cancer: Some cancer cells have impaired HRR, leading to a higher frequency of DNA mutations and alterations. This deficiency can be exploited for therapeutic purposes.
Components of the HRD Score: The HRD score is typically calculated based on several genetic and genomic features, including the extent of loss of heterozygosity (LOH), the number of telomeric allelic imbalances (TAI), and large-scale state transitions (LST) in the tumor’s DNA.
- Loss of Heterozygosity (LOH): LOH refers to the loss of one copy of a gene in a specific region of a chromosome. It can result from a deletion or other genetic alterations. High LOH is associated with HRD.
- Telomeric Allelic Imbalances (TAI): TAI involves imbalances in the number of alleles near telomeres (the protective ends of chromosomes). TAI is often indicative of genomic instability and HRD.
- Large-Scale State Transitions (LST): LST measures the number of transitions between regions of DNA copy number gain and loss in the tumor genome. Frequent LST events are associated with HRD.
Clinical Implications: A high HRD score in a tumor suggests that the cancer cells have a deficiency in homologous recombination repair, making them vulnerable to treatments that target DNA repair mechanisms. This includes therapies like PARP (Poly ADP-ribose polymerase) inhibitors, which can further inhibit DNA repair in HRD-deficient cells, leading to cell death.
Treatment with PARP Inhibitors: PARP inhibitors have been approved for certain cancers, particularly those with BRCA mutations and high HRD scores. These inhibitors block an alternative DNA repair pathway in cancer cells with HRD, causing them to accumulate DNA damage and eventually die.
Research and Clinical Trials: HRD testing and scoring are also used in clinical trials to identify patients who may benefit from investigational treatments targeting HRD in various cancer types.

In summary, the HRD score is a valuable tool for assessing DNA repair deficiency within cancer cells. It plays a critical role in predicting the response to certain targeted therapies, particularly PARP inhibitors, and can guide treatment decisions in oncology. The HRD score provides insights into the tumor’s biology and its susceptibility to treatments that exploit DNA repair deficiencies.

HLA typing High resolution (Single person):

HLA typing, or Human Leukocyte Antigen typing, is a genetic test that determines an individual’s specific HLA alleles or variants at high resolution. HLA genes are located on chromosome 6 and play a crucial role in the immune system by encoding proteins that help the immune system recognize and distinguish between self and foreign substances, including pathogens and transplanted tissues or organs.

High-resolution HLA typing provides detailed information about an individual’s HLA alleles, which can have important clinical and research applications, including:

Organ and Stem Cell Transplantation: HLA typing is essential in organ and stem cell (bone marrow or hematopoietic stem cell) transplantation to ensure compatibility between the donor and recipient. A high-resolution HLA match reduces the risk of graft rejection and graft-versus-host disease (GVHD) in stem cell transplantation.
Hematology and Oncology: HLA typing can be used in hematological disorders, such as leukemia, lymphoma, and certain autoimmune diseases. It may help identify suitable donors for bone marrow or stem cell transplantation in these cases.
Autoimmune Diseases: Some autoimmune diseases, such as ankylosing spondylitis and celiac disease, are associated with specific HLA alleles. HLA typing can aid in the diagnosis and management of these conditions.
Pharmacogenetics: Certain HLA alleles are associated with drug sensitivities and adverse reactions. HLA typing can help guide medication selection and dosing to minimize adverse effects and improve treatment outcomes.
Population Genetics and Anthropology: HLA typing is also used in population genetics and anthropology to study human genetic diversity and migration patterns.
Research and Drug Development: High-resolution HLA typing is crucial in research related to infectious diseases, cancer immunotherapy, and the development of personalized therapies.

High-resolution HLA typing provides a detailed and precise assessment of an individual’s HLA alleles, often at the allelic or nucleotide level. This level of resolution is crucial in transplantation and other clinical applications, where even minor differences in HLA profiles can have significant clinical implications.

The specific method used for HLA typing may vary, but it typically involves DNA analysis from blood or tissue samples. The results are reported as a combination of HLA alleles at each of the HLA loci (e.g., HLA-A, HLA-B, HLA-DRB1, etc.), providing a comprehensive profile of an individual’s HLA genotype. High-resolution HLA typing is typically performed by specialized laboratories and requires expertise in the field of immunogenetics.

Whole Exome Sequencing:

Whole exome sequencing (WES) is a powerful genetic sequencing technique used to identify and analyze the protein-coding regions of an individual’s genome. These protein-coding regions are known as exons and represent only a small fraction of the entire genome. Here’s an overview of whole exome sequencing:

Genome Division: The human genome consists of approximately 3 billion base pairs of DNA. It contains both coding and non-coding regions. Whole exome sequencing focuses on the coding regions, which make up only about 1-2% of the entire genome but contain the instructions for producing proteins.
Exon Sequencing: WES involves the selective sequencing of all exons in an individual’s genome. Exons are the segments of DNA that are transcribed into messenger RNA (mRNA) and then translated into proteins. These regions are crucial because mutations or variations within exons can lead to various genetic disorders and diseases.
Targeted Capture: To perform WES, DNA is extracted from a patient’s sample (usually blood or saliva), and a process called targeted capture is used. In targeted capture, DNA probes are designed to bind specifically to the exonic regions of the genome. These probes “capture” the exonic DNA, which is then sequenced.
High-Throughput Sequencing: After the exonic DNA is captured, high-throughput sequencing technologies, such as Illumina sequencing, are used to determine the sequence of nucleotide bases (A, T, C, G) in these regions. This generates a massive amount of data.
Data Analysis: The sequencing data is then analyzed using specialized bioinformatics tools and software to identify genetic variations, including single nucleotide variations (SNVs) and small insertions or deletions (indels), within the exonic regions.
Clinical and Research Applications: WES has a wide range of applications in both clinical and research settings. It is used to diagnose rare genetic disorders, identify disease-causing mutations, and understand the genetic basis of various conditions, including cancer, neurological disorders, and metabolic diseases.
Cost-Effective: WES is more cost-effective than whole genome sequencing (WGS) because it selectively focuses on the most functionally significant portions of the genome. It allows for the identification of clinically relevant mutations without sequencing the entire genome.
Limitations: While WES is highly valuable, it does have limitations. It may miss mutations or variations in non-coding regions of the genome, regulatory elements, and structural variations (such as large insertions, deletions, and rearrangements). For a comprehensive view of an individual’s entire genome, whole genome sequencing is necessary.

In summary, whole exome sequencing is a targeted approach to genetic sequencing that focuses on the protein-coding regions of the genome. It is a valuable tool for diagnosing genetic disorders, understanding disease mechanisms, and conducting research into the genetic basis of various conditions.

Clinical Exome Sequencing:

Clinical exome sequencing (CES) is a specialized form of genetic testing that focuses on sequencing the protein-coding regions of an individual’s genome, known as exons, for the purpose of diagnosing suspected genetic disorders. CES is performed in a clinical setting, often as part of the diagnostic workup for patients with unexplained or rare medical conditions. Here’s what you need to know about clinical exome sequencing:

Exon Sequencing: CES selectively targets and sequences the exons of the human genome, which represent approximately 1-2% of the entire genome but contain the vast majority of disease-causing mutations. These exons are responsible for coding the proteins that carry out essential functions in the body.
Clinical Indications: CES is typically ordered when a patient presents with a complex, undiagnosed medical condition that is suspected to have a genetic basis. This may include congenital disorders, developmental delays, intellectual disabilities, metabolic disorders, and a wide range of rare and genetic diseases.
Sample Collection: To perform CES, a sample of the patient’s DNA is collected, usually from a blood sample or, in some cases, from saliva or other tissue sources.
Sequencing Technology: High-throughput DNA sequencing technologies, such as next-generation sequencing (NGS), are used to sequence the exonic regions of the patient’s genome. These technologies generate massive amounts of DNA sequence data.
Bioinformatics Analysis: The raw sequencing data is processed and analyzed using specialized bioinformatics tools and software. This analysis identifies genetic variations, including single nucleotide variations (SNVs) and small insertions or deletions (indels), within the exonic regions.
Variant Interpretation: After identifying genetic variants, a critical step in CES is variant interpretation. Genetic counselors and clinical geneticists review the variants to determine their clinical relevance and whether they are likely to be disease-causing.
Diagnostic Yield: CES has a variable diagnostic yield, which depends on factors such as the patient’s clinical presentation, the specific genetic disorder suspected, and the quality of the sequencing and analysis. The diagnostic yield can range from around 25% to 50% or more for certain conditions.
Clinical Reporting: Clinicians receive a report detailing any identified pathogenic or likely pathogenic variants that may explain the patient’s clinical symptoms. The report may also include recommendations for further clinical evaluation, management, or genetic counseling.
Genetic Counseling: Genetic counseling is an essential component of CES. Genetic counselors help patients and families understand the implications of genetic testing results, provide information about the genetic condition, and assist with decision-making regarding family planning and medical management.
Research and Discovery: CES data can contribute to ongoing genetic research and the discovery of novel disease-causing genes and mutations.

In summary, clinical exome sequencing is a valuable tool in the diagnosis of genetic disorders with complex or rare presentations. It enables healthcare providers to identify disease-causing genetic mutations and provide patients and families with accurate diagnoses and appropriate medical management strategies.

MLH1 Promoter Methylation:

MLH1 promoter methylation refers to a specific epigenetic modification that can occur in the MLH1 gene. The MLH1 gene is one of the DNA mismatch repair (MMR) genes, and it plays a crucial role in maintaining the integrity of the DNA by correcting errors that occur during DNA replication. When the MLH1 gene is not functioning properly due to mutations or other changes, it can lead to microsatellite instability (MSI) and an increased risk of certain types of cancer, particularly colorectal cancer.

Promoter methylation is an epigenetic modification that involves the addition of methyl groups to the promoter region of a gene. The promoter region is responsible for controlling the gene’s expression, determining when and how much of the gene’s protein product is produced.

In the context of MLH1 promoter methylation:

Silencing of MLH1 Gene: Methylation of the MLH1 gene’s promoter region can result in the gene being “silenced” or turned off. When the promoter is methylated, the gene is less likely to be transcribed into messenger RNA (mRNA), and consequently, less MLH1 protein is produced.
Impact on DNA Repair: Reduced MLH1 protein production can impair the DNA mismatch repair (MMR) mechanism. As a result, errors in DNA replication and recombination may not be corrected effectively, leading to microsatellite instability (MSI). MSI is characterized by the accumulation of mutations in repetitive DNA sequences, and it is a hallmark of certain types of cancer, especially colorectal cancer.
Cancer Risk: MLH1 promoter methylation is often associated with an increased risk of developing colorectal cancer and other cancers that are linked to MMR deficiencies. It can be both a somatic event (occurring within a tumor) or a germline event (inherited).
Diagnostic and Prognostic Marker: Detection of MLH1 promoter methylation can serve as a diagnostic and prognostic marker in cancer. It is frequently assessed in colorectal cancer and can help guide treatment decisions and predict clinical outcomes.
Epigenetic Therapy: In some cases, the reversal of promoter methylation through epigenetic therapy (e.g., with demethylating agents) may be considered as a therapeutic strategy to reactivate the MLH1 gene and restore normal DNA repair function in cancer cells.

It’s important to note that MLH1 promoter methylation is just one mechanism that can lead to MLH1 inactivation and MMR deficiency. Genetic mutations within the MLH1 gene itself can also result in loss of function and an increased cancer risk.

Detection and analysis of MLH1 promoter methylation are typically performed through molecular diagnostic techniques, such as methylation-specific polymerase chain reaction (MSP) or bisulfite sequencing, in the context of cancer diagnosis and risk assessment. Understanding the epigenetic changes, like promoter methylation, that impact DNA repair genes like MLH1 can have important implications for cancer prevention, diagnosis, and treatment.

MGMT Promoter Methylation:

MGMT promoter methylation is an epigenetic modification that occurs in the promoter region of the MGMT (O-6-methylguanine-DNA methyltransferase) gene. The MGMT gene plays a crucial role in DNA repair by removing alkyl groups from the O-6 position of guanine in DNA. Methylation of the MGMT promoter can have important implications in cancer development and treatment. Here’s what you need to know:

Promoter Methylation: Promoter methylation involves the addition of methyl groups to the promoter region of a gene. The promoter is responsible for controlling the gene’s expression, determining when and how much of the gene’s protein product is produced. Methylation of the promoter region can lead to gene silencing, where the gene is turned off or expressed at lower levels.
MGMT Gene Function: The MGMT gene encodes a DNA repair enzyme that removes alkyl groups, such as those caused by alkylating agents in chemotherapy or environmental exposures, from DNA. This repair process prevents DNA damage and mutations.
Impact on DNA Repair: When the MGMT gene’s promoter is methylated, the gene is often silenced, and the production of the MGMT enzyme is reduced or eliminated. This can result in decreased DNA repair capacity, as the damaged DNA is not efficiently repaired, and mutations can accumulate.
Cancer and MGMT Methylation: MGMT promoter methylation is commonly observed in various types of cancer, including glioblastoma multiforme (a type of brain cancer), colorectal cancer, and certain types of lung and hematological cancers. In some cases, MGMT methylation is associated with the response to chemotherapy and patient prognosis.
Response to Chemotherapy: MGMT promoter methylation can impact the response to alkylating chemotherapy agents, such as temozolomide. When MGMT is silenced due to methylation, cancer cells are less able to repair DNA damage caused by these agents, making them more sensitive to treatment.
Prognostic Marker: In glioblastoma, for example, the presence of MGMT promoter methylation is often associated with a more favorable response to treatment and improved survival outcomes. It can serve as a prognostic marker in guiding treatment decisions.
Predictive Marker: MGMT promoter methylation status is used as a predictive marker to identify patients who are likely to benefit from alkylating chemotherapy. Patients with MGMT methylation may be more responsive to these treatments.
Testing: MGMT promoter methylation status is typically determined through molecular diagnostic techniques, such as methylation-specific polymerase chain reaction (MSP) or pyrosequencing, in clinical laboratories. It is an essential part of the diagnostic workup and treatment planning in specific cancer types.

In summary, MGMT promoter methylation is an epigenetic alteration that can affect DNA repair mechanisms and influence cancer development and treatment outcomes. Understanding the methylation status of the MGMT gene can guide treatment decisions, particularly in the context of chemotherapy, and provide valuable information for cancer prognosis and management.

Histopathology- Final Diagnosis (Including H&E, IHC):

Histopathology of a large specimen refers to the microscopic examination of a tissue or organ sample that is relatively large in size. This type of histopathological examination is commonly used in clinical medicine and research to diagnose diseases, understand the nature of abnormalities, and study various conditions affecting tissues and organs. Here’s an overview of histopathology with a focus on large specimens:

Sample Collection: The first step in histopathology involves collecting a tissue or organ sample from a patient. The sample can be obtained through various methods, including surgical procedures, biopsies, or autopsies. Large specimens are typically obtained during surgeries or other procedures that involve the removal of significant tissue or organs.
Fixation: After collection, the tissue specimen is usually immediately fixed in a formalin solution. Fixation helps preserve the tissue’s cellular structure and prevents degradation. The duration of fixation depends on the size and type of the specimen.
Processing: The fixed tissue specimen undergoes a series of processing steps, including dehydration, clearing, and embedding in paraffin wax. These steps prepare the tissue for thin sectioning.
Sectioning: The tissue is cut into thin slices, known as histological sections or slides, using a microtome. Large specimens may require special equipment or techniques to obtain thin sections consistently.
Staining: Histological sections are stained with various dyes, such as hematoxylin and eosin (H&E) or specific immunohistochemical stains, to highlight different tissue components and structures. Staining is crucial for visualizing cellular details and abnormalities.
Microscopic Examination: The stained histological sections are examined under a light microscope by a pathologist or histotechnologist. The pathologist assesses various characteristics, including cell morphology, tissue architecture, and the presence of abnormalities or disease processes.
Diagnosis: Based on the microscopic findings, the pathologist makes a diagnosis or provides a detailed report. This report may include information about the nature of the disease, its extent, and any recommendations for further tests or treatment.
Clinical Applications: Histopathology of large specimens is used in various clinical applications, such as the diagnosis of cancer, assessment of surgical margins, evaluation of organ function, and identification of infectious diseases.
Research: Large specimen histopathology is also essential in research settings. It allows scientists to study tissue samples in detail, investigate disease mechanisms, and develop new diagnostic and therapeutic approaches.
Quality Control: Ensuring the accuracy and quality of histopathological examinations is crucial. Laboratories often have quality control measures in place to maintain high standards, including regular proficiency testing for pathologists and technical staff.

In summary, histopathology of large specimens plays a vital role in medical diagnosis, patient care, and research. It involves the collection, preparation, staining, microscopic examination, and interpretation of tissue or organ samples to provide valuable insights into various diseases and conditions.

Histopathology – Medium Specimen:

Histopathology of a medium-sized specimen involves the microscopic examination of a tissue or organ sample that is of moderate size. This type of histopathological examination is commonly used in clinical medicine and research to diagnose diseases, understand the nature of abnormalities, and study various conditions affecting tissues and organs. Here’s an overview of histopathology with a focus on medium-sized specimens:

Sample Collection: The first step in histopathology involves collecting a tissue or organ sample from a patient. The sample can be obtained through various methods, including biopsies, surgical procedures, or autopsies. Medium-sized specimens are typically obtained during procedures that involve the removal of a moderate amount of tissue or organs.
Fixation: After collection, the tissue specimen is usually immediately fixed in a formalin solution. Fixation helps preserve the tissue’s cellular structure and prevents degradation. The duration of fixation depends on the size and type of the specimen.
Processing: The fixed tissue specimen undergoes a series of processing steps, including dehydration, clearing, and embedding in paraffin wax. These steps prepare the tissue for thin sectioning.
Sectioning: The tissue is cut into thin slices, known as histological sections or slides, using a microtome. Medium-sized specimens may require less time and effort to obtain thin sections compared to large specimens.
Staining: Histological sections are stained with various dyes, such as hematoxylin and eosin (H&E) or specific immunohistochemical stains, to highlight different tissue components and structures. Staining is crucial for visualizing cellular details and abnormalities.
Microscopic Examination: The stained histological sections are examined under a light microscope by a pathologist or histotechnologist. The pathologist assesses various characteristics, including cell morphology, tissue architecture, and the presence of abnormalities or disease processes.
Diagnosis: Based on the microscopic findings, the pathologist makes a diagnosis or provides a detailed report. This report may include information about the nature of the disease, its extent, and any recommendations for further tests or treatment.
Clinical Applications: Histopathology of medium-sized specimens is used in various clinical applications, such as the diagnosis of cancer, assessment of surgical margins, evaluation of organ function, and identification of infectious diseases.
Research: Medium-sized specimen histopathology is also essential in research settings. It allows scientists to study tissue samples in detail, investigate disease mechanisms, and develop new diagnostic and therapeutic approaches.
Quality Control: Ensuring the accuracy and quality of histopathological examinations is crucial. Laboratories often have quality control measures in place to maintain high standards, including regular proficiency testing for pathologists and technical staff.

In summary, histopathology of medium-sized specimens plays a vital role in medical diagnosis, patient care, and research. It involves the collection, preparation, staining, microscopic examination, and interpretation of tissue or organ samples to provide valuable insights into various diseases and conditions.

Histopathology of cell blocks and fine-needle aspiration cytology (FNAC) are specialized techniques used in pathology and clinical medicine to examine and diagnose various medical conditions, especially cancer. These methods allow for the assessment of cellular and tissue abnormalities at the microscopic level. Here’s an overview of histopathology involving cell blocks and FNAC:

Cell Blocks:

Collection of Specimen: Cell blocks are typically prepared from fluid specimens, such as pleural effusions, ascites, pericardial effusions, or cyst fluids. These fluids may contain abnormal cells, which need to be examined in detail.
Centrifugation: The fluid specimen is centrifuged to concentrate the cells at the bottom of the container. This step separates the cells from the fluid.
Cell Pellet: After centrifugation, a cell pellet containing the concentrated cells is obtained.
Fixation: The cell pellet is then fixed with formalin, similar to tissue fixation in traditional histopathology. Fixation helps preserve cellular morphology.
Processing: The fixed cell pellet is processed in a manner similar to traditional tissue specimens. It is dehydrated, cleared, and embedded in paraffin wax.
Sectioning: Thin sections are cut from the paraffin-embedded cell block, and these sections are stained with various dyes for microscopic examination.
Microscopic Examination: A pathologist examines the stained cell block sections under a microscope. They assess cell morphology, tissue architecture, and the presence of any abnormalities, such as cancer cells.
Diagnosis: Based on the microscopic findings, the pathologist makes a diagnosis or provides a detailed report, often related to the presence of cancer or other cellular abnormalities.

FNAC (Fine-Needle Aspiration Cytology):

Procedure: FNAC is a minimally invasive diagnostic procedure. A fine, thin needle is inserted directly into a suspicious mass or lesion, such as a tumor or lymph node.
Aspiration: The needle is used to aspirate (withdraw) a small sample of cells from the lesion. This sample may contain both normal and abnormal cells.
Slide Preparation: The aspirated material is smeared onto glass slides or collected in a fixative solution, depending on the laboratory’s preferred method.
Staining: The collected cells on the slides are stained, often with H&E stain, to enhance the visualization of cellular details.
Microscopic Examination: A cytotechnologist or pathologist examines the stained FNAC slides under a microscope. They assess the cellular characteristics and look for abnormalities, such as cancer cells.
Diagnosis: Based on the cellular morphology observed, the cytotechnologist or pathologist provides a diagnosis or report. FNAC is frequently used to diagnose or rule out cancer, determine the type of cancer, and guide treatment decisions.

Both cell blocks and FNAC play crucial roles in diagnosing various medical conditions, particularly cancer. They are valuable tools for obtaining cellular and tissue information, allowing for early detection, accurate diagnosis, and the formulation of appropriate treatment plans. These techniques are often used in conjunction with other diagnostic methods, such as imaging studies and blood tests, to provide a comprehensive assessment of a patient’s health.

Brain Panel Comprehensive genomic profiling with TMB, MSI, IDH1/2, MGMT Methylation, ATRX, TP53, 1p/19 co-deletion. Ki-67:

The “Brain Panel Comprehensive Genomic Profiling” you mentioned includes various genetic and genomic markers that are important for the diagnosis, classification, and treatment planning of brain tumors, particularly gliomas and other central nervous system (CNS) neoplasms. Let’s break down the components of this panel:

Tumor Mutation Burden (TMB): TMB is a measure of the total number of genetic mutations in a tumor’s DNA. High TMB can be associated with increased susceptibility to certain immunotherapies.
Microsatellite Instability (MSI): MSI is a measure of genetic instability in the tumor, often resulting from defects in DNA mismatch repair (MMR). It is more commonly associated with certain types of cancer, but it can have implications for treatment selection.
IDH1/2: Isocitrate dehydrogenase (IDH) genes are frequently mutated in gliomas. Mutations in these genes can help classify gliomas into different subtypes and guide treatment decisions.
MGMT Methylation: Methylation of the MGMT promoter can lead to reduced expression of the MGMT protein, which is involved in DNA repair. MGMT methylation status is an important prognostic and predictive marker in glioblastoma, as it can influence response to temozolomide chemotherapy.
ATRX: ATRX is a gene that, when mutated, is associated with a specific subtype of glioma called astrocytoma. ATRX mutations can impact tumor classification and prognosis.
TP53: TP53 is a tumor suppressor gene frequently mutated in many types of cancer, including gliomas. TP53 mutations can influence tumor behavior and prognosis.
1p/19q Codeletion: Codeletion of chromosome arms 1p and 19q is a characteristic genetic alteration seen in oligodendrogliomas, a subtype of glioma. It has both diagnostic and prognostic significance.
Ki-67: Ki-67 is a protein marker used to assess the proliferative activity of tumor cells. High Ki-67 expression often indicates more aggressive tumors.

This comprehensive genomic profiling panel provides a wealth of information about the genetic and molecular characteristics of brain tumors. It allows oncologists and pathologists to:

Accurately classify brain tumors into specific subtypes, which can guide treatment decisions.
Predict patient prognosis and determine appropriate therapeutic strategies.
Identify potential targets for precision therapies and immunotherapies.
Assess the potential for DNA repair mechanisms and response to chemotherapy, such as with MGMT methylation status.

Each of these markers contributes to a more precise understanding of the tumor’s biology and can inform personalized treatment plans for patients with brain tumors. This type of genomic profiling is becoming increasingly important in oncology as it allows for tailored treatments based on the unique genetic makeup of each patient’s tumor.

Test A-Z

1) Liquid Biopsy (CTC):

2) Her2-neu by FISH:

3) C-MYC FISH:

4) BCL-6 by FISH:

5) BCL-2 by FISH:

6) ALK by FISH:

7) ROS1 by FISH:

8) ROS1 by FISH:

9) N-MYC by FISH:

10) Combo MYC & BCL2 by FISH:

11) 1p/19q codeletion:

11) Diffuse large B cell lymphoma:

Breast biopsy with ER, PR & Her-2:

Her2-neu by IHC:

Ki-67(Mib-1) By IHC:

Microsatellite Instability (MSI) by IHC:

PDL-1 (22C3) by IHC:

ALK by IHC:

ROS1 by IHC:

ER,PR, Her2-neu:

NIPT:

NIPT with Micro Deletions:

BRCA 1&2 Deletion & Duplication:

Somatic Panel- 50 Gene:

Somatic Panel- 161 Gene- POLE & NTRK:

Somatic Panel for CA Endometrium:

Somatic Panel Comprehensive genomic profiling with TMB, MSI, DNA and RNA- 590 Genes:

Tumor Mutation Burden (TMB):

BRCA 1 & 2 Somatic Panel:

Leukemia Panel NGS- 40 Genes and 29 fusions (DNA and RNA):

Liquid Biopsy (ctDNA)- 50 genes:

Hereditary Cancer Gene Panel:

Mutation Specific Gene Test:

HRR Gene Panel:

HRR Gene Panel:

HLA typing High resolution (Single person):

Whole Exome Sequencing:

Clinical Exome Sequencing:

MLH1 Promoter Methylation:

MGMT Promoter Methylation:

Histopathology- Final Diagnosis (Including H&E, IHC):

Histopathology – Medium Specimen:

Cell Blocks:

FNAC (Fine-Needle Aspiration Cytology):

Brain Panel Comprehensive genomic profiling with TMB, MSI, IDH1/2, MGMT Methylation, ATRX, TP53, 1p/19 co-deletion. Ki-67:

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