Glioma 1p/19q Co-deletion FISH Test at Chughtai Lab

Glioma 1p/19q Co-deletion (FISH) at Chughtai Lab

The Glioma 1p/19q Co-deletion test using Fluorescence In Situ Hybridization (FISH) is a highly specialized molecular pathology investigation performed to characterize brain tumors, specifically diffuse gliomas. This advanced genetic test detects the simultaneous loss of the short arm of chromosome 1 (1p) and the long arm of chromosome 19 (19q). This specific genetic alteration, known as an unbalanced translocation t(1;19)(q10;p10), is the defining molecular signature of oligodendrogliomas. At Chughtai Lab, this test is executed using state-of-the-art cytogenetic technology to assist neuro-oncologists, neuropathologists, and neurosurgeons across Pakistan in establishing an accurate diagnosis, predicting therapeutic response, and determining patient prognosis.

Fluorescence In Situ Hybridization (FISH) works by utilizing fluorescently labeled DNA probes that specifically bind (hybridize) to complementary target sequences on chromosomes 1 and 19 within the tumor cell nuclei. By examining the hybridized tissue under a specialized fluorescence microscope, molecular pathologists can count the signals and determine if the 1p and 19q chromosomal regions are present or deleted. This molecular evaluation has become a cornerstone of modern neuro-oncology, particularly following the World Health Organization (WHO) classification guidelines for tumors of the central nervous system, which mandate molecular profiling alongside traditional histological examination.

The clinical importance of the Glioma 1p/19q Co-deletion FISH test cannot be overstated. It provides critical diagnostic value by distinguishing oligodendrogliomas from other types of gliomas, such as astrocytomas or glioblastomas, which may look similar under a standard light microscope but behave very differently clinically. Furthermore, the presence of the 1p/19q co-deletion is a powerful predictive biomarker, indicating that the tumor is highly likely to respond favorably to specific chemotherapeutic regimens, such as alkylating agents (temozolomide or the PCV regimen consisting of procarbazine, lomustine, and vincristine), as well as radiation therapy. Consequently, this test directly influences the personalized treatment strategy designed for each patient.

Clinical Procedure: What to Expect

Patient Preparation

Because the Glioma 1p/19q Co-deletion (FISH) test is performed on tumor tissue obtained during a surgical procedure, the preparation requirements differ significantly from standard blood or urine tests:

• No Direct Patient Fasting: The patient does not need to fast or undergo any special physical preparation for this laboratory test itself, as it is performed on an existing tissue sample.
• Tissue Sample Acquisition: The test requires a formalin-fixed paraffin-embedded (FFPE) tissue block or unstained tissue slides obtained from a previous brain biopsy or surgical resection.
• Retrieval of Pathology Materials: If the biopsy or surgery was performed at a different hospital, the patient or their family must retrieve the paraffin block (FFPE block) and the corresponding histopathology report from that facility and submit them to Chughtai Lab.
• Clinical History Submission: It is highly recommended to provide a copy of the initial histopathology report, relevant neuroimaging reports (such as brain MRI), and a brief clinical history to assist the molecular pathology team in their evaluation.

During the Procedure

The laboratory analysis of the tissue specimen involves several highly controlled technical steps performed by specialized cytogenetic technologists at Chughtai Lab:

• Sectioning: The paraffin block containing the tumor tissue is cut into extremely thin sections (typically 4 to 5 micrometers thick) and mounted on positively charged glass slides.
• Deparaffinization and Pretreatment: The tissue slides undergo deparaffinization and enzymatic digestion to break down protein barriers, allowing the fluorescent DNA probes to access the target DNA within the cell nuclei.
• Denaturation and Hybridization: The tumor DNA and the fluorescently labeled probes (specifically targeting the 1p36 and 19q13 regions, along with control probes for the 1q25 and 19p13 regions) are heated to denature the double-stranded DNA. They are then incubated together overnight to allow the probes to hybridize to their target sequences.
• Post-Hybridization Washing: The slides are washed to remove any unbound or non-specifically bound probes, ensuring high specificity of the fluorescent signals.
• Counterstaining: The cell nuclei are stained with a fluorescent blue dye called DAPI (4',6-diamidino-2-phenylindole) to make them visible under the microscope.
• Microscopic Analysis: A molecular pathologist examines the slides using a high-resolution fluorescence microscope equipped with specialized filters. The pathologist counts the fluorescent signals in at least 100 non-overlapping, intact tumor nuclei to calculate the ratio of target-to-control signals, determining whether a co-deletion is present.

When is a Glioma 1p/19q co-deletion(FISH) Performed?

Classification of Diffuse Gliomas

Physicians request this test when a patient is diagnosed with a diffuse glioma. Under the current WHO guidelines, a definitive diagnosis of oligodendroglioma cannot be made based on microscopic appearance alone; it requires the objective genetic demonstration of both an IDH mutation and the 1p/19q co-deletion. This test is essential to classify the tumor accurately within the molecular taxonomy of brain cancers.

Distinguishing Oligodendroglioma from Astrocytoma

In many cases, diffuse astrocytomas and oligodendrogliomas exhibit overlapping histological features, making them difficult to differentiate using standard hematoxylin and eosin (H&E) staining. Because astrocytomas do not typically harbor the 1p/19q co-deletion, performing FISH allows pathologists to clearly distinguish between these two entities, which carry distinct clinical courses and treatment pathways.

Predicting Response to Chemotherapy and Radiotherapy

Neuro-oncologists utilize the 1p/19q co-deletion status as a predictive biomarker to guide therapeutic decisions. Patients whose tumors exhibit the co-deletion show significantly higher sensitivity and prolonged response to chemotherapy (particularly alkylating agents) and radiation therapy compared to those with intact chromosomes, helping clinicians select the most effective treatment regimen.

Prognostic Stratification in Brain Tumors

The presence of the 1p/19q co-deletion is a highly favorable prognostic indicator. Gliomas with this genetic profile are generally slow-growing and associated with significantly longer median survival times—often measured in decades—compared to non-deleted gliomas. Identifying this marker helps physicians provide patients and families with more accurate expectations regarding the disease course.

Evaluation of Recurrent or Atypical Brain Lesions

When a brain tumor recurs or presents with atypical clinical and radiological features, clinicians may order this test on the recurrent tissue or re-evaluate the primary specimen. Confirming the molecular status helps determine if the recurrent lesion is a progression of the original oligodendroglioma or if it has undergone clonal evolution, guiding subsequent salvage therapies.

What Does a Glioma 1p/19q co-deletion(FISH) Detect?

The Glioma 1p/19q Co-deletion FISH test evaluates the genetic status of specific chromosomal regions within the tumor cells. The test can detect several distinct genetic patterns and clinical findings, including:

• Complete 1p/19q Co-deletion: The simultaneous loss of the 1p36 locus and the 19q13 locus across the evaluated tumor cells, confirming the molecular hallmark of oligodendroglioma.
• Intact 1p and 19q Loci: Normal retention of both chromosomal arms, which points away from a diagnosis of classical oligodendroglioma and suggests other glioma subtypes.
• Isolated 1p Deletion: Loss of the 1p region with retention of the 19q region, a pattern occasionally seen in astrocytomas or other neuroepithelial tumors.
• Isolated 19q Deletion: Loss of the 19q region with retention of the 1p region, which may occur in various non-oligodendroglial brain tumors.
• Polysomy of Chromosome 1: An increased number of copies of both the target (1p36) and control (1q25) signals, indicating chromosomal instability or polyploidy.
• Polysomy of Chromosome 19: Multiple copies of both the 19q13 and 19p13 loci within the tumor nuclei.
• Monosomy of Chromosome 1: The presence of only a single copy of chromosome 1 in the tumor cells, rather than the normal pair.
• Monosomy of Chromosome 19: The presence of only a single copy of chromosome 19.
• Relative Loss of 1p36: A ratio of the 1p36 probe to the 1q25 control probe of less than 0.8, indicating a deletion of the short arm.
• Relative Loss of 19q13: A ratio of the 19q13 probe to the 19p13 control probe of less than 0.8, indicating a deletion of the long arm.
• Normal Diploid Status: Two signals for each of the four probes (1p, 1q, 19p, 19q) in the majority of analyzed cells, representing a normal genetic complement.
• Intratumoral Genetic Heterogeneity: Variations in the deletion status across different areas of the tumor specimen, indicating a mixed cell population.
• Segmental Deletions: Partial deletions of the 1p or 19q arms that do not involve the entire chromosomal arm, which may have different clinical implications than complete arm deletions.
• Amplification of Control Loci: An abnormal increase in the control signals (1q25 or 19p13) relative to the target signals.
• Technical Artifacts: Identification of issues such as tissue autofluorescence, probe precipitation, or poor tissue preservation that may require a repeat test or alternative block.
• Low Tumor Cell Content: Insufficient neoplastic cells within the sample slide, indicating that the selected area of the block may not be representative of the tumor.
• Normal Tissue Contamination: High presence of non-neoplastic cells (like normal astrocytes, microglia, or blood vessels) that can dilute the deletion signal ratio.
• Homozygous Deletion: Complete absence of both copies of a specific locus, which is a rare but highly significant genetic finding.
• Structural Rearrangements: Complex chromosomal translocations or inversions involving chromosomes 1 or 19.
• Copy Number Variations (CNVs): Broad alterations in the copy numbers of the evaluated genetic regions, reflecting the overall genomic instability of high-grade tumors.

Turnaround Time and Report Access at Chughtai Lab

Because molecular pathology testing involves complex tissue processing, enzymatic digestion, overnight hybridization, and manual enumeration under a fluorescence microscope by specialized pathologists, the turnaround time for the Glioma 1p/19q Co-deletion (FISH) test at Chughtai Lab is typically 7 to 10 working days. This timeline ensures that every step of the quality control protocol is meticulously followed to deliver highly accurate and reliable results.

Once the report is finalized and signed off by the consultant molecular pathologist, Chughtai Lab provides multiple convenient ways for patients and clinicians to access the results. An automated SMS notification is sent to the registered mobile number containing a direct link to download the report. Patients can also access their diagnostic reports online through the official Chughtai Lab website portal or by using the Chughtai Lab mobile application. Physical copies of the reports can be collected from any Chughtai Lab medical center or collection point across Pakistan.

Glioma 1p/19q co-deletion(FISH) Findings Overview

Structure / Parameter Evaluated	Normal Findings	Possible Abnormal Findings
1p36 Locus Status	Intact (Two signals per nucleus)	Deleted (One or zero signals per nucleus, ratio < 0.8)
19q13 Locus Status	Intact (Two signals per nucleus)	Deleted (One or zero signals per nucleus, ratio < 0.8)
1p/19q Co-deletion Profile	Both loci intact (No co-deletion)	Simultaneous deletion of both 1p and 19q loci
Chromosome 1 Ploidy	Diploid (Two control signals)	Polysomy (Three or more signals) or Monosomy (One signal)
Chromosome 19 Ploidy	Diploid (Two control signals)	Polysomy (Three or more signals) or Monosomy (One signal)
Signal Ratio (Target/Control)	Ratio between 0.9 and 1.1	Ratio < 0.8 (Definitive deletion)
Tumor Cell Percentage	High tumor cellularity (> 70%)	Low cellularity or high contamination with normal brain tissue
Genomic Stability	Stable diploid pattern	High genomic instability, complex structural rearrangements

Note: Diagnostic findings should always be interpreted by a qualified healthcare professional together with the patient’s symptoms, medical history, physical examination, laboratory investigations, previous imaging studies, and other relevant clinical information. Additional investigations or specialist consultation may be recommended depending on the findings.

Why Choose Chughtai Lab for Glioma 1p/19q co-deletion(FISH)?

• Experienced Healthcare Professionals: The test is performed and interpreted by highly trained cytogeneticists and consultant molecular pathologists with extensive experience in neuro-oncology.
• Patient-Focused Care: Chughtai Lab prioritizes patient convenience, offering clear guidance on tissue block submission and hassle-free report delivery.
• Quality Diagnostic Services: Operating under strict international laboratory standards, ensuring high clinical accuracy and reproducibility of molecular results.
• Professional Reporting: Reports are structured comprehensively, providing clear visual data, signal ratios, and clinical interpretations aligned with WHO guidelines.
• Modern Diagnostic Approach: Utilizing advanced fluorescence microscopes and high-specificity FDA-approved DNA probes for precise hybridization.
• Comfortable Environment: Dedicated customer support teams are available at all major centers to assist patients with their inquiries and sample tracking.
• Convenient Location: With a vast network of collection centers across Pakistan, patients can easily submit their pathology blocks close to home.
• Commitment to Accurate Diagnosis: Chughtai Lab is dedicated to providing timely, evidence-based diagnostic insights that form the foundation of effective cancer treatment.