The ‘Cancer Genomics Laboratory’ (CGL) is a ‘one-stop’ genomics core facility for researchers at TTCRC and clinical investigators at Tata Medical Center. The overarching goal of CGL is to provide state-of-the-art infrastructure and technical expertise adept to deliver high-quality genomic data from a comprehensive range of cutting-edge genomic services like sequencing, SNP array and customised disease tracking assays (PReDiCT).

Our centralized facility houses high-throughput sequencing platforms like MiSeq, NextSeq 550 (Illumina), MinION and PromethION 2 Solo (Oxford Nanopore Technologies) and the conventional 8- capillary 3500 Genetic Analyzer (ABI). Besides, basic equipment required for quality check and quantification of nucleic acids are available like NanoDrop 2000 Spectrophotometer, Qubit 3.0 and Qubit 4.0 Fluorometer, 4200 TapeStation System – Automated Electrophoresis, Veriti and Proflex Thermal Cyclers, StepOnePlus Real-Time PCR System for 96-well (with VeriFlex block), QuantStudio 7 Flex Real-Time PCR System for both 96- and 384-well and ChemiDoc XRS+ system.

Therapeutic drug monitoring (TDM) is crucial in pharmacometric research, particularly for optimizing therapy. At TTCRC, we conduct specialized pharmacological studies to identify the most therapeutically effective Asparaginases for treating acute lymphoblastic leukaemia.

Asparaginase Activity Assay

We measure enzyme activity in patient samples using a validated AHA-Indooxine assay, complying with international analytical assay standards/guidelines. This allows to identify if plasma drug concentrations are above the therapeutic threshold, aiding clinicians to take informed decision.

Asparaginase Antibody Assay

Utilizes a standardized ELISA method to identify anti-Asparaginase and anti-PEG IgG antibodies, signalling potential enzyme inactivation or hypersensitivity responses.

The lab is currently involved in optimising clinical proteomic assays to estimate blood plasma metabolite concentrations using Mass Spectrometry and developing population pharmacokinetic models for dose optimization and individualization.

The Flow Cytometry Facility at TTCRC facility is equipped with advanced instruments, including the BD FACSARIA Fusion™ (SORP), a flow cytometer sorter with 5 lasers (UV, violet, blue, yellow-green, red) and 18 detection channels, enabling sorting of up to 4 populations simultaneously in tubes or plates, and operates at Biosafety Level 2 (BSL-2). Additionally, the BD Accuri™ C6 Plus, a benchtop flow cytometer analyzer with 2 lasers and 4 detection channels (FL1, FL2, FL3, FL4).

For magnetic cell sorting, the facility uses the Miltenyi Biotec MACS sorter.The Thermo Scientific ARCTIC Refrigerated/Heated Bath Circulator maintains cell viability by regulating temperatures between 5°C and 40°C.

The facility offers cell phenotyping and sorting services to both TTCRC and external researchers. External users are welcome to access the facility on Mondays and Fridays. For scheduling and further inquiries about services with the BD FACSARIA Fusion™ system, external users can contact Mrs. Bhaswati Tarafdar at bhaswati.tarafdar@ttcrc.tmckolkata.org

This facility is an invaluable resource for researchers requiring advanced flow cytometry techniques for their cellular analysis and sorting needs.

*Costing for different type for FACS ARIA Fusion™ experiment with GST

Type of Flow Cytometric Experiment	Costing after including GST (CGST 09% and SGST 09%)
Flow cytometric acquisition without FlowJo analysis	Rs. 3000.00
Flow cytometric acquisition with FlowJo analysis	Rs. 3250.00
Flow cytometric Sorting experiment without FlowJo analysis	Rs. 4700.00
Flow cytometric Sorting experiment with FlowJo analysis	Rs. 5000.00

Mass Spectrometer

Currently our facility is equipped with TripleTOF 6600 mass spectrometer (AB Sciex), connected to a nano LC system (Eksigent) coupled with a nano electrospray ion source for bottom-up MS-based proteomics.

Key Features:

• 1. Time-of-flight (TOF) Mass Analyzer
• 2. Data Acquisition: DDA (Data Dependent Acquisition) and DIA (Data Independent Acquisition), upto 200 variable SWATH windows per cycle.
• 3. Scan speed: 100 Hz MS/MS scans per sec in DDA Acquisition; upto 200 MS/MS scans per sec in SWATH Acquisition
• 4. Mass resolution-30,000 high-resolution TOF MS/MS mode
• 5. Nano LC for acquisition of clinical and low input samples ranging from 500ng -1ug of sample load.

Softwares

• 1. Analyst version 1.7.1 for MS data acquisition
• 2. Peak View version 2.2 for analysis and assessing data files

Capabilities

• 1. Clinical Proteomics
• 2. Drug metabolism studies
• 3. Plasma biomarker studies

Laser Capture Microdissection (LCM)

We are equipped with Leica LMD7 Microscope in our facility.

Specifications:

• Laser Microdissection (LMD): High precision, contamination-free laser microdissection and sample collection
• Microscope Type: Fully automated upright research microscope
• Laser Options: 355 nm UV laser for precise cutting
• Illumination: LED illumination for brightfield, phase contrast, and fluorescence
• Objective Lenses: Broad range of objectives from 2.5X till 150X, including high NA objectives for detailed imaging
• Camera Options: High-resolution digital cameras for imaging and documentation
• Software Compatibility: Leica Application Suite (LAS) for advanced imaging and analysis
• Future possibilities of AI integrated interface applications

Applications: The Leica LMD7 is ideal for a wide range of applications including genomics, proteomics, and single-cell analysis. It is suitable for use in fields such as cancer research, neuroscience, and plant biology.

Software:

• Leica Application Suite X (LAS X): Comprehensive software platform for advanced imaging and analysis
• Leica Laser Microdissection Software: Specialized software for controlling the laser microdissection process and managing dissected samples