Foundation One Liquid at Chughtai Lab

Foundation One Liquid at Chughtai Lab

FoundationOne® Liquid CDx is a state-of-the-art, FDA-approved comprehensive genomic profiling (CGP) test that analyzes circulating cell-free DNA (cfDNA) from a simple blood draw. This advanced liquid biopsy is designed to identify genomic alterations across 324 genes, offering critical therapeutic insights for patients diagnosed with advanced or metastatic solid tumors. Chughtai Lab, Pakistan’s premier diagnostic network, offers this highly specialized molecular test across its extensive nationwide network, including major hubs such as Lahore, Karachi, Islamabad, Rawalpindi, and Peshawar. By analyzing circulating tumor DNA (ctDNA) shed by cancer cells into the bloodstream, this test provides a minimally invasive alternative to traditional tissue biopsies, enabling oncologists to design highly personalized treatment strategies based on the unique genetic profile of a patient’s cancer.

The clinical utility of FoundationOne Liquid CDx lies in its ability to detect four main classes of genomic alterations: base substitutions, insertions and deletions (indels), copy number alterations (CNAs), and genomic rearrangements. Additionally, the test evaluates complex genomic signatures, such as blood Tumor Mutational Burden (bTMB) and Microsatellite Instability (MSI), which are critical biomarkers for predicting response to immunotherapies. For patients with advanced malignancies, obtaining a tissue biopsy can often be challenging, risky, or clinically impossible due to tumor location or the patient’s overall health. Foundation One Liquid at Chughtai Lab bypasses these limitations, requiring only a peripheral blood sample to deliver comprehensive, actionable genomic data that can guide targeted therapy, immunotherapy, and clinical trial enrollment.

Clinical Procedure: What to Expect

Patient Preparation

Preparing for the Foundation One Liquid CDx test at Chughtai Lab is straightforward and designed to minimize patient stress. Because this is a blood-based molecular test, the preparation requirements differ significantly from those of imaging studies or invasive tissue biopsies. Patients should observe the following guidelines to ensure a smooth collection process:

• No Fasting Required: Patients do not need to fast before the blood draw. You may eat and drink normally prior to your appointment.
• Hydration: It is highly recommended to drink plenty of water before the procedure. Proper hydration dilutes the blood slightly and plumps the veins, making venipuncture easier and more comfortable.
• Medication: Continue taking all prescribed medications as directed by your physician. There is generally no need to discontinue any therapeutic regimens, though you should inform the clinical staff of any ongoing treatments.
• Required Documentation: Patients must present a valid doctor’s prescription, a copy of their latest histopathology or diagnostic report, and a completed clinical history form. A signed patient consent form is also mandatory for molecular genetic testing.
• Kit Availability: Ensure that the specialized FoundationOne Liquid CDx specimen collection kit is reserved and available at your selected Chughtai Lab branch prior to your visit.

During the Procedure

The blood collection procedure is performed by highly trained phlebotomists at Chughtai Lab who are specifically certified in handling specialized molecular diagnostic kits. The process is quick, safe, and follows strict international protocols:

• Patient Positioning: You will be seated comfortably in a blood collection chair. The phlebotomist will inspect your arm to locate a suitable vein, typically in the antecubital fossa (the crook of the elbow).
• Sanitization: The skin over the selected vein is thoroughly cleansed with an antiseptic swab to prevent any contamination of the sample.
• Sample Collection: Using a sterile, single-use needle, the phlebotomist will perform a standard venipuncture. The FoundationOne Liquid CDx kit requires the collection of two specialized tubes of blood (approximately 8.5 mL per tube). These tubes contain a proprietary preservative that prevents the lysis of nucleated blood cells, ensuring that the cell-free DNA remains stable during transit.
• Inversion and Mixing: Immediately after collection, the phlebotomist will gently invert the tubes 8 to 10 times to ensure the blood mixes thoroughly with the preservative.
• Duration: The entire venipuncture process takes less than 5 to 10 minutes.
• Post-Collection Care: A small bandage or adhesive strip will be applied to the puncture site. You will be asked to apply gentle pressure for a few minutes to prevent bruising.
• Sample Logistics: The collected samples are documented, packaged in accordance with strict international cold-chain and bio-safety regulations, and dispatched directly to the accredited Foundation Medicine laboratory for advanced next-generation sequencing (NGS) analysis.

When is a Foundation One Liquid Performed?

Advanced or Metastatic Non-Small Cell Lung Cancer (NSCLC)

In patients diagnosed with advanced or metastatic non-small cell lung cancer, identifying driver mutations is crucial for selecting first-line targeted therapies. Oncologists frequently order Foundation One Liquid at Chughtai Lab to screen for actionable alterations in genes such as EGFR, ALK, ROS1, RET, MET, and BRAF. Detecting these mutations allows patients to receive highly effective oral tyrosine kinase inhibitors (TKIs) instead of conventional chemotherapy, significantly improving progression-free survival and quality of life.

Metastatic Breast Cancer

For patients with advanced or metastatic breast cancer, understanding the evolving genomic landscape of the tumor is vital for therapeutic selection. This test is performed to identify mutations in genes like PIK3CA, ESR1, and BRCA1/2. Identifying a PIK3CA mutation can qualify a patient for targeted therapies such as alpelisib in combination with endocrine therapy, while ESR1 mutations help clinicians detect resistance to aromatase inhibitors and guide subsequent endocrine treatment adjustments.

Advanced Prostate Cancer

In metastatic castration-resistant prostate cancer (mCRPC), identifying alterations in homologous recombination repair (HRR) genes is essential. Clinicians utilize Foundation One Liquid to detect mutations in BRCA1, BRCA2, ATM, and other HRR pathway genes. Patients harboring these genetic alterations may benefit significantly from targeted treatment with PARP inhibitors, such as olaparib or rucaparib, which exploit the tumor’s DNA repair deficiencies to induce cancer cell death.

Ovarian and Colorectal Cancers

Foundation One Liquid is highly valuable in managing advanced ovarian and colorectal cancers. In ovarian cancer, it identifies BRCA1/2 mutations and homologous recombination deficiencies to guide maintenance therapy with PARP inhibitors. In colorectal cancer, the test profiles KRAS, NRAS, and BRAF mutations. Identifying these mutations is critical, as patients with wild-type KRAS/NRAS may benefit from anti-EGFR monoclonal antibodies, whereas those with mutations are resistant to these therapies.

Solid Tumors with Limited Tissue Availability

One of the primary clinical indications for liquid biopsy is when a patient’s tumor tissue is exhausted, insufficient, or entirely inaccessible. Repeat surgical biopsies carry inherent risks, costs, and delays. Foundation One Liquid provides a comprehensive genomic profile using a simple blood draw, allowing oncologists to make timely, evidence-based treatment decisions without subjecting the patient to invasive tissue extraction procedures.

What Does a Foundation One Liquid Detect?

Foundation One Liquid CDx utilizes advanced next-generation sequencing (NGS) to analyze circulating cell-free DNA (cfDNA) isolated from plasma. The test is designed to detect a wide array of clinically relevant genomic alterations and signatures, including:

• EGFR Mutations: Including sensitizing mutations (Exon 19 deletions, L858R) and resistance mutations (T790M, C797S) in non-small cell lung cancer.
• ALK Gene Fusions: Rearrangements that predict response to ALK inhibitors like alectinib or brigatinib.
• ROS1 and RET Fusions: Actionable rearrangements guiding targeted tyrosine kinase inhibitor therapy.
• BRAF V600E Mutations: Found in melanoma, colorectal cancer, and non-small cell lung cancer, guiding BRAF/MEK inhibitor combinations.
• BRCA1 and BRCA2 Alterations: Germline or somatic mutations that predict sensitivity to PARP inhibitors in breast, ovarian, prostate, and pancreatic cancers.
• PIK3CA Mutations: Guiding the use of PI3K inhibitors in hormone receptor-positive, HER2-negative breast cancer.
• KRAS and NRAS Mutations: Predictive biomarkers for resistance to anti-EGFR therapies in colorectal cancer.
• MET Exon 14 Skipping Mutations: Actionable targets in advanced non-small cell lung cancer.
• NTRK1, NTRK2, and NTRK3 Fusions: Tumor-agnostic biomarkers that qualify patients for TRK inhibitors like larotrectinib.
• ERBB2 (HER2) Amplifications and Mutations: Guiding anti-HER2 targeted therapies in breast, gastric, and lung cancers.
• ESR1 Mutations: Indicating resistance to standard aromatase inhibitors in breast cancer.
• ATM, PALB2, and CHEK2 Mutations: Other homologous recombination repair genes involved in DNA damage response.
• KIT and PDGFRA Mutations: Crucial for therapeutic selection in gastrointestinal stromal tumors (GIST).
• FGFR1, FGFR2, and FGFR3 Alterations: Actionable targets in cholangiocarcinoma and urothelial carcinoma.
• Microsatellite Instability (MSI): A genomic signature indicating high MSI (MSI-H), which predicts a favorable response to immune checkpoint inhibitors.
• blood Tumor Mutational Burden (bTMB): A measure of the number of somatic mutations per megabase of sequenced DNA, serving as a predictor for immunotherapy efficacy.

Turnaround Time and Report Access at Chughtai Lab

Due to the highly sophisticated nature of next-generation sequencing and the international logistics involved, the turnaround time for Foundation One Liquid at Chughtai Lab is typically 14 to 21 days from the date of sample collection. Once the blood sample is collected at a Chughtai Lab facility, it undergoes strict quality control checks before being securely shipped to the accredited Foundation Medicine laboratory. After the genomic sequencing and bioinformatics analysis are complete, a detailed, comprehensive clinical report is generated. This report lists all detected genomic alterations, associated FDA-approved targeted therapies, potential clinical trials, and relevant resistance markers. The final report is delivered directly to the patient’s referring oncologist and can also be accessed securely by the patient or physician through the Chughtai Lab online portal and mobile application.

Foundation One Liquid Findings Overview

Structure / Parameter Evaluated	Normal Findings	Possible Abnormal Findings
EGFR Gene Status	Wild-type (No alterations detected)	Exon 19 deletions, L858R point mutations, T790M resistance mutations, Exon 20 insertions
ALK Gene Status	No rearrangements or fusions detected	EML4-ALK fusions or other actionable ALK gene rearrangements
BRCA1 / BRCA2 Genes	No pathogenic alterations detected	Somatic or germline pathogenic mutations, insertions, or deletions indicating homologous recombination deficiency
PIK3CA Gene Status	Wild-type (No alterations detected)	Activating mutations in Exon 9 or Exon 20 (e.g., H1047R, E545K, E542K)
KRAS / NRAS Genes	Wild-type (No alterations detected)	Mutations in codons 12, 13, 61, 117, or 146 (predicting resistance to anti-EGFR therapy)
NTRK1 / 2 / 3 Genes	No fusion transcripts detected	NTRK gene fusions (tumor-agnostic biomarkers for TRK inhibitor therapy)
Microsatellite Instability (MSI)	Microsatellite Stable (MSS)	Microsatellite Instability-High (MSI-H), indicating eligibility for immunotherapy
blood Tumor Mutational Burden (bTMB)	Low bTMB (Fewer mutations per megabase)	High bTMB (Elevated mutation count, predicting favorable response to immune checkpoint inhibitors)

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 Foundation One Liquid?

• CAP Accredited Central Laboratory: Chughtai Lab’s central facility holds prestigious College of American Pathologists (CAP) accreditation, ensuring the highest international standards of quality and accuracy.
• Official Collaboration: Chughtai Lab works in close coordination with Roche Pakistan to provide authentic, reliable Foundation Medicine testing services.
• Expert Phlebotomy Services: Highly trained and certified phlebotomists ensure precise sample collection using specialized molecular diagnostic kits.
• Robust Cold-Chain Logistics: Strict temperature-controlled logistics are maintained to preserve sample integrity during international transit to Foundation Medicine.
• Nationwide Accessibility: With a vast network of collection centers across Pakistan, patients can easily access this advanced test in Lahore, Karachi, Islamabad, and other major cities.
• Secure Online Portal: Patients and oncologists can access comprehensive diagnostic reports securely through the Chughtai Lab website and mobile app.
• Dedicated Molecular Pathology Support: Access to professional guidance and customer support to assist patients through the documentation and booking process.
• Patient-Centric Care: A compassionate and professional environment designed to make the diagnostic journey as comfortable and seamless as possible for cancer patients.