The Biospecimen Processing Laboratory specializes in the comprehensive processing of blood and a wide range of other human biospecimens. Blood samples are carefully fractionated into plasma, serum, buffy coat, and red blood cells using state-of-the-art liquid handling automation platforms that enable efficient processing and aliquoting of high sample volumes. In addition to blood, the lab processes tissues, oral rinse, saliva, buccal brushings, hair, nails, urine, and faecal samples. Strict verification protocols are followed for all incoming samples, and biospecimens are stored long-term in a BioBank at -80°C to ensure integrity. The laboratory also performs nucleic acid (DNA/RNA) extraction from a variety of sample types including blood, oral rinse, tissue, and faecal matter. Extractions are carried out both manually and through automated platforms, with downstream quality and quantity assessments performed using Nanodrop (absorbance-based) and Qubit (fluorescence-based) quantification methods. With a strong focus on precision, scalability, and sample integrity, the laboratory supports high-quality biobanking and molecular research.

Exposure assessment laboratory leads nutritional assessment efforts. 24-hour dietary recalls are commonly used in low-resource, low literacy settings, they are time and resource intensive when aiming to estimate usual intake. To address this, the lab is validating a Food Frequency Questionnaire (FFQ) used in established cohorts, leveraging a recently developed nutrient database and standardized validation protocols. Validation will be supported by multiple 24-hour recalls, allowing for refinement of the FFQ to better capture long-term dietary intake across India’s diverse cultural and dietary landscapes. In addition, the laboratory conducts specialized bioassessments for infections such as Helicobacter pylori (H. pylori) and Human Papillomavirus (HPV). For infectious disease profiling, the lab assesses Helicobacter pylori and HPV using PCR-based methods for detection and genotyping, supported by antigen testing, urea breath tests (for H. pylori), and immunohistochemistry when applicable. These techniques allow evaluation of both presence and virulence.

A. Inductively Coupled Plasma Mass Spectrometry (ICP-MS): Heavy metals, particularly arsenic, cadmium, chromium, lead, mercury, and nickel, are linked to an increased risk of cancer and are classified as carcinogens by the International Agency for Research on Cancer (IARC). These metals can disrupt DNA synthesis and repair, induce oxidative stress, and alter epigenetic mechanisms, all contributing to tumour development. Our lab utilizes state of the art mass spectrometry techniques for quantifying trace heavy metals in numerous biological samples like Whole Blood, Saliva, Serum, and Urine. These highly sensitive techniques allow us to perform multi-element analysis and attain detection limits of as low as parts per trillion (ppt). This method converts a liquid sample into a fine aerosol and is further atomised and ionised using high temperature plasma. The respective sample ions are filtered through two Quadrupoles and a Collision reaction cell (CRC) to detect based on mass/charge ratio. An accurate estimation is possible by multiple mass filtering steps with utmost sensitivity and reproducibility. With such advanced equipment, we can contribute in the detection of various heavy metals that could be hazardous even in trace amounts.

B. High Pressure Liquid Chromatography (HPLC): Aflatoxins, particularly Aflatoxin B1, B2, G1, and G2, are potent toxic compounds linked to an increased risk of cancer. The International Agency for Research on Cancer (IARC), a specialized agency of the World Health Organization (WHO), has classified these aflatoxins as Group 1 carcinogens, confirming their carcinogenicity to humans. To detect and quantify aflatoxins with high precision, our laboratory employs a state-of-the-art, advanced form of high-pressure liquid chromatography. This method utilizes high pressure to enhance separation efficiency, resolution, sensitivity, and reproducibility. We apply this sophisticated analytical technique to a variety of biological samples, including whole blood, saliva, serum, and urine. Aflatoxin present in samples separate based on interactions with the stationary phase, and a fluorescence detector measures their characteristic signals. This technique offers numerous advantages, including high resolution, sensitivity, speed, and reproducibility, making it a widely used analytical technique across various fields. It is capable of detecting a broad range of analytes, and can be coupled with other analytical techniques like mass spectrometry (MS) for enhanced capabilities mainly speciation of certain compounds.

C. Biomarkers: Biomarkers are measurable indicators of biological processes, disease states, or treatment responses. They play a crucial role in clinical practice by enabling early diagnosis (e.g., troponin for myocardial infarction), monitoring disease progression (e.g., CRP for inflammation), assessing disease risk (e.g., lipid profile for cardiovascular risk), guiding therapeutic decisions (e.g., HER2 in breast cancer), and predicting prognosis (e.g., tumour markers in oncology). Creatinine and cystatin C are commonly used to estimate glomerular filtration rate (GFR), while lipid profile and CRP provide insights into cardiovascular risk and inflammation. Currently, we are estimating specific biomarkers (Creatinine, CRP, Lipid Profile and Cystatin C) which are used to assess kidney function, lipid metabolism, and inflammation. Creatinine and Cystatin C are enzymatically estimated whereas Lipid profile and CRP are evaluated using advanced turbidimetric immunoassays.

The High Throughput Genotyping Laboratory is equipped with advanced instruments and automated platforms that enable the processing of large sample volumes with high precision and reproducibility. Our lab performs gene expression analysis to quantify RNA levels, allowing simultaneous assessment of thousands of genes and providing valuable insights into gene regulation, cellular processes, and disease mechanisms. We also conduct genome-wide association studies (GWAS) using microarray technology to identify genetic variants associated with complex traits and diseases across large populations. This approach helps pinpoint genetic regions linked to observable traits and potential therapeutic targets. In addition, our lab offers a range of next-generation sequencing (NGS) services. Targeted sequencing focuses on specific genes or regions, providing a cost-effective, high-coverage method ideal for validating GWAS results or investigating candidate genes. Exome sequencing targets all protein-coding regions of the genome, which make up about 1–2% of the genome but harbor most known disease-causing mutations. Shotgun sequencing involves random fragmentation of DNA followed by sequencing and assembly, suitable for de novo genome assembly and metagenomic studies. For the most comprehensive analysis, whole genome sequencing (WGS) captures the entire DNA sequence, including coding and non-coding regions. These sequencing technologies are supported by robust bioinformatics pipelines that facilitate efficient data processing, variant detection, and functional interpretation. With its high-throughput capabilities, our laboratory can scale up to large population studies, delivering detailed and reliable genomic data. By integrating multiple genomic approaches, we provide critical insights that drive advancements in genetic research and personalized medicine.

One of the core functions of the Centre for Cancer Epidemiology (CCE) is the development and maintenance of robust databases to support research studies. This involves designing efficient database structures, implementing them using advanced tools, and ensuring their ongoing performance, security, and reliability. The CCE team leverages a range of technologies—including Java, JavaScript, C#, MS SQL, MySQL, and MS Access—to design and implement systems tailored to the specific needs of various studies. These systems provide centralised, organised data storage that facilitates quick retrieval, seamless analysis, and efficient reporting. The use of scalable solutions ensures the databases can manage growing data volumes and user loads. Additionally, programming languages like C#, Java, and JavaScript are employed to build both web-based and standalone applications interfaced with SQL databases, while MS Access serves as a practical option for smaller, user-friendly systems with graphical interfaces. Regular maintenance activities such as performance tuning, backups, and security updates ensure that the databases remain robust and responsive to the demands of ongoing and future research initiatives.