BRCA 1/2 Genetic Analysis by NGS at Chughtai Lab

BRCA 1/2 Genetic Analysis by NGS at Chughtai Lab

The BRCA 1/2 Genetic Analysis by NGS at Chughtai Lab is a highly sophisticated molecular diagnostic test designed to identify germline mutations in the BRCA1 and BRCA2 genes. These two genes are critical tumor suppressors responsible for maintaining genomic stability. They produce proteins that play a vital role in repairing damaged DNA, specifically double-strand breaks, through a highly precise pathway known as homologous recombination. When a pathogenic mutation occurs in either the BRCA1 or BRCA2 gene, the DNA repair mechanism is compromised, leading to an accumulation of genetic errors, genomic instability, and a significantly elevated risk of developing breast, ovarian, pancreatic, prostate, and other associated cancers.

Next-Generation Sequencing (NGS) represents the gold standard in modern molecular diagnostics. Unlike older sequencing methods that analyze one DNA fragment at a time, NGS allows for the high-throughput, parallel sequencing of millions of DNA fragments simultaneously. This technology provides comprehensive coverage of all coding exons and adjacent intron-exon boundaries of both the BRCA1 and BRCA2 genes. By utilizing NGS, Chughtai Lab can detect a wide spectrum of genetic alterations, including single nucleotide variants (SNVs), small insertions or deletions (indels), and copy number variations (CNVs) with exceptional sensitivity and specificity. This test is of paramount clinical importance, as it empowers individuals with a high risk of hereditary cancers to make informed decisions regarding surveillance, risk-reducing strategies, and targeted therapeutic interventions.

Clinical Procedure: What to Expect

Patient Preparation

Proper preparation is essential to ensure the accuracy of the BRCA 1/2 Genetic Analysis by NGS and to help patients navigate the emotional and clinical implications of genetic testing. Patients should observe the following guidelines:

• Pre-Test Genetic Counseling: It is highly recommended that patients undergo genetic counseling with a qualified genetic counselor or oncologist prior to testing. This session helps patients understand the benefits, limitations, and potential psychological impact of the results.
• Informed Consent: Genetic testing requires formal written consent. Patients must read and sign a consent form acknowledging that they understand the purpose of the test and the potential implications of positive, negative, or uncertain results.
• No Fasting Required: There are no dietary restrictions or fasting requirements for this test. Patients can eat and drink normally before the sample collection.
• Medical History Documentation: Patients should provide a detailed personal and family history of cancer, including the types of cancer diagnosed, ages of onset, and any previous genetic testing results of family members.
• Blood Transfusion History: Patients who have received a recent blood transfusion (especially within the last 3 to 4 weeks) must inform the laboratory, as donor DNA can interfere with the accuracy of the germline genetic analysis. In such cases, testing may need to be delayed or performed using an alternative sample type, such as a buccal swab.

During the Procedure

The sample collection process for the BRCA 1/2 Genetic Analysis by NGS is straightforward, safe, and minimally invasive. The procedure involves the following steps:

• Patient Identification and Verification: The phlebotomist will verify the patient’s identity using at least two independent identifiers (e.g., full name and date of birth) and confirm that the signed consent form is present.
• Venipuncture: A trained phlebotomist will locate a suitable vein, typically in the antecubital fossa of the arm. The skin over the vein is thoroughly cleansed with an antiseptic solution to prevent contamination.
• Sample Collection: A small volume of peripheral blood (approximately 3 to 5 mL) is drawn into a sterile tube containing ethylenediaminetetraacetic acid (EDTA) as an anticoagulant. EDTA preserves the integrity of the genomic DNA within the white blood cells.
• Post-Collection Care: Once the blood is drawn, the needle is removed, and gentle pressure is applied to the puncture site with a sterile gauze pad to stop any bleeding. A small bandage is then applied.
• Laboratory Processing: The collected blood sample is securely labeled with a unique barcode and transported to the molecular biology department. Here, genomic DNA is extracted from the leukocytes, quantified, and subjected to library preparation, target enrichment, NGS sequencing, and bioinformatic analysis.

When is a BRCA 1/2 Genetic Analysis by NGS Performed?

Family History of Breast or Ovarian Cancer

Physicians frequently order the BRCA 1/2 Genetic Analysis by NGS for individuals who have a strong family history of breast or ovarian cancer. This includes having multiple close relatives (such as a mother, sister, or daughter) diagnosed with breast cancer, particularly if the diagnoses occurred at an early age (under 50). A family history of ovarian cancer at any age is also a strong clinical indicator. Identifying a familial pathogenic variant allows other family members to undergo targeted testing to determine their own risk profile.

Personal Diagnosis of Early-Onset or Triple-Negative Breast Cancer

A personal history of breast cancer diagnosed at age 50 or younger is a primary clinical indication for genetic testing. Furthermore, patients diagnosed with triple-negative breast cancer (cancers that lack estrogen receptors, progesterone receptors, and HER2 protein expression) at or before age 60 are highly encouraged to undergo BRCA testing. Triple-negative breast cancers are statistically more likely to be associated with BRCA1 mutations, and knowing the mutation status is critical for guiding surgical decisions and systemic therapies.

Personal or Family History of Ovarian, Pancreatic, or Prostate Cancer

The clinical utility of BRCA testing extends beyond breast cancer. Ovarian cancer, particularly high-grade serous carcinoma, is strongly linked to BRCA1 and BRCA2 mutations. Consequently, all patients diagnosed with epithelial ovarian, fallopian tube, or primary peritoneal cancer are candidates for testing, regardless of age or family history. Additionally, a personal or family history of pancreatic cancer or aggressive, metastatic prostate cancer warrants BRCA testing, as these malignancies are known components of the Hereditary Breast and Ovarian Cancer (HBOC) syndrome spectrum.

Evaluation for Targeted Cancer Therapies (e.g., PARP Inhibitors)

For patients already diagnosed with advanced, recurrent, or metastatic cancers, BRCA 1/2 genetic status serves as a vital predictive biomarker. Poly (ADP-ribose) polymerase (PARP) inhibitors, such as olaparib and talazoparib, are targeted therapies that exploit the concept of synthetic lethality in cells with defective homologous recombination repair (such as BRCA-mutated cancer cells). Identifying a germline BRCA mutation allows oncologists to prescribe these highly effective targeted agents, significantly improving progression-free survival in eligible patients.

Assessment of Hereditary Cancer Syndromes in High-Risk Populations

Certain ethnic populations exhibit a significantly higher prevalence of specific BRCA1 and BRCA2 mutations, known as founder mutations. For example, individuals of Ashkenazi Jewish descent have a 1 in 40 chance of carrying a BRCA mutation, compared to approximately 1 in 400 in the general population. In individuals with this ancestry, even a limited family history of cancer can justify performing a comprehensive BRCA 1/2 Genetic Analysis by NGS to proactively assess hereditary cancer risks.

What Does a BRCA 1/2 Genetic Analysis by NGS Detect?

The BRCA 1/2 Genetic Analysis by NGS is designed to detect a wide array of genetic variations within the coding regions and splice sites of the BRCA1 and BRCA2 genes. The findings may include:

• Pathogenic variants in the BRCA1 gene
• Pathogenic variants in the BRCA2 gene
• Likely pathogenic variants in the BRCA1 gene
• Likely pathogenic variants in the BRCA2 gene
• Variants of Uncertain Significance (VUS) in the BRCA1 gene
• Variants of Uncertain Significance (VUS) in the BRCA2 gene
• Likely benign variants (not typically reported)
• Benign variants (not typically reported)
• Frameshift mutations resulting in premature stop codons
• Nonsense mutations leading to truncated, non-functional proteins
• Missense mutations causing single amino acid substitutions
• Splice donor site mutations affecting mRNA splicing
• Splice acceptor site mutations affecting mRNA splicing
• Large genomic deletions encompassing one or more exons
• Large genomic duplications encompassing one or more exons
• In-frame insertions or deletions (indels)
• Single nucleotide polymorphisms (SNPs)
• Regulatory or promoter region variants
• Germline mutations present in all cells of the body
• Specific founder mutations (e.g., BRCA1 c.68_69delAG)
• Absence of any detectable pathogenic or likely pathogenic variants

Turnaround Time and Report Access at Chughtai Lab

Chughtai Lab is committed to providing accurate and timely diagnostic services. Because Next-Generation Sequencing (NGS) is a highly complex molecular procedure requiring extensive laboratory processing, high-throughput sequencing, and detailed bioinformatic analysis, the turnaround time for the BRCA 1/2 Genetic Analysis by NGS is typically 3 to 4 weeks. This duration ensures that every identified variant is meticulously analyzed, cross-referenced with international genetic databases, and classified according to the stringent guidelines of the American College of Medical Genetics and Genomics (ACMG).

Patients can easily access their diagnostic reports through Chughtai Lab’s advanced digital infrastructure. Once the report is finalized and signed off by a Consultant Molecular Pathologist, patients receive an automated SMS notification. Reports can be downloaded directly from the official Chughtai Lab website or via the user-friendly Chughtai Lab mobile application. Physical copies of the reports can also be collected from any of Chughtai Lab’s numerous diagnostic centers located across Pakistan, or delivered directly to the patient’s home through their dedicated report delivery service.

BRCA 1/2 Genetic Analysis by NGS Findings Overview

Structure / Parameter Evaluated	Normal Findings	Possible Abnormal Findings
BRCA1 Gene Coding Regions	No pathogenic or likely pathogenic variants detected.	Pathogenic or likely pathogenic single nucleotide variants, insertions, or deletions.
BRCA2 Gene Coding Regions	No pathogenic or likely pathogenic variants detected.	Pathogenic or likely pathogenic single nucleotide variants, insertions, or deletions.
Intron-Exon Boundaries	Intact consensus splice donor and acceptor sequences.	Splice-site mutations resulting in aberrant mRNA splicing and non-functional proteins.
Large Genomic Rearrangements (CNVs)	Normal copy number (two copies of each exon).	Large deletions or duplications of one or more exons in BRCA1 or BRCA2.
Variant Classification (ACMG)	Classified as Benign (Class 1) or Likely Benign (Class 2).	Classified as Pathogenic (Class 5), Likely Pathogenic (Class 4), or Variant of Uncertain Significance (Class 3).
Clinical Significance	Average population risk of developing breast and ovarian cancers.	Significantly elevated lifetime risk of breast, ovarian, pancreatic, and prostate cancers.
Mutation Type	Wild-type sequence or synonymous variant with no functional impact.	Frameshift, nonsense, missense, or splice-site mutations causing protein truncation.

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 BRCA 1/2 Genetic Analysis by NGS?

• Experienced Healthcare Professionals: Chughtai Lab features a team of highly qualified molecular biologists, bioinformaticians, and Consultant Pathologists who specialize in genetic interpretation.
• State-of-the-Art Technology: The molecular diagnostics department is equipped with advanced, high-throughput Next-Generation Sequencing (NGS) platforms to ensure maximum accuracy.
• Patient-Focused Care: Chughtai Lab prioritizes patient comfort, confidentiality, and clear communication throughout the genetic testing process.
• Quality Diagnostic Services: The laboratory adheres to strict international quality control standards and participates in external proficiency testing programs.
• Professional Reporting: Reports are structured in accordance with ACMG guidelines, providing clear, actionable clinical insights for oncologists and genetic counselors.
• Convenient Location and Access: With a vast network of collection centers across Pakistan, patients can easily access testing services near their homes.
• Home Sample Collection: Chughtai Lab offers a reliable and professional home sample collection service, allowing patients to have their blood drawn in the comfort of their homes.
• Digital Report Delivery: Patients can instantly access, download, and share their genetic reports via the Chughtai Lab mobile app, website, or WhatsApp.