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CoTeRI
Core Technologies Research Initiative

The National Institute of Biomedical Genomics (NIBMG) is a publicly-funded national institution. NIBMG’s mantra is Accelerating Genomics for Health. To accelerate genomics, NIBMG believes that, to the extent possible, all its facilities must be made available for academic pursuits of scientists of all publicly-funded institutions in India.

To facilitate pursuit of genomics, NIBMG shall help to scientists of other publicly-funded institutions in India – primarily, but not exclusively, on a collaborative mode – by providing access to its high-end, high-throughput technology platforms.

 

 

How to Access

Accessing technology platforms (details provided below) of NIBMG is easy. If you are associated with a publicly-funded institution/university in India, all that you need to do is to arrange for the reagents and consumables required for running your samples and generating the data. There are no hidden costs. NIBMG pays for manpower, electricity, water, instrumentation usage costs, etc. Consultations on data analysis are also provided. Anyone intending to use any of these platforms must plan their work in consultation with Dr. Arindam Maitra (coteri@nibmg.ac.in, +91-9903380808). NIBMG will accord higher priority to work on human biomedical genetics and genomics. You are also welcome to contact any faculty member of NIBMG (http://www.nibmg.ac.in) to engage in prior discussion about conducting your research collaboratively that will automatically place your work at a higher priority in respect of core facility access.

 

Current Platforms

Technology Platforms

  • Massively-parallel, Ultra High-throughput DNA Sequencers

    • HiSeq-2500 & 2000 short-read platforms (Illumina)

    • Ion Proton platform (Life Technologies)

    • GS-FLX long-read platforms (Roche)

  • Moderately High-throughput DNA Sequencing Platform

    • Ion Torrent PGM (Life Technologies)

  • Genome wide Genotyping and Gene Expression Microarray Platform

    • iScan (Illumina)

  • Real-Time PCR Platform

    • ABI 7900HT (Life Technologies)

    • Lightcycler 480 (Roche)

  • Capillary Sequencing Platform

    • ABI 3500XL (Life Technologies)

  • Multiplex Suspension Array Platform

    • Bio-Plex 200 (Bio-Rad)

Data Analysis and Storage Infrastructure

The high performance computing and centralized data storage services of NIBMG are operated on 24x7 mode from a Data Centre located inside the institute. The facility consists of the following components:

  • 300 TB Grid Scalar Central Data Storage platform (DDN)

  • IlluminaCompute high performance system for analysis of HiSeq-2000 sequence data

  • Four high performance parallel computing Clusters (PSSC Lab) for analysis of DNA GS-FLX sequence data

  • DL380 server, HP Proliant DL380 G6 servers with 2 Intel Xeon 2.40 GHz quad core processors and 64 GB memory

  • DL580 server, HP Proliant DL580 G7 servers with 8 Intel Xeon 2.27 GHz eight core processors and 128 GB memory

  • HP Z400 Workstation with Intel Xeon 2.67 GHz quad core processor and 8 GB memory

  • HP Z800 Workstation with Intel Xeon 2.66 GHz six core processor and 24 GB memory

  • HP Proliant 360 G7 servers with Intel Xeon 2.66 GHz quad core processor and 32 GB memory

  • High performance computing cluster with eight HP BL460c blade servers, each blade server with 2 quad core processors and 64 GB memory

  • HP Storage Works Ultrium 1760 SAS magnetic tape backup facility

  • 10 GBPS Ethernet network

 

 

Wet Lab Activities

DNA Sequencing

DNA sequencing has a broad range of applications such as the discovery and confirmation of SNPs, identification of rare variants and the identification of insertions, deletions and chromosomal re-arrangements. This Platform generates massively parallel sequencing data using HiSeq-2500 and 2000 (Illumina), Ion Proton and Ion Torrent PGM (Life Technologies) and GS-FLX (Roche-454) for the following applications:

Whole Genome Sequencing

This is the sequencing of whole genomes where the sequence reads are mapped against a published reference sequence e.g. HG19. The total sequencing data output is based on the required depth at which the genome has to be sequenced. For example, for whole human genome of size 3 GB, sequencing at an average depth of 30X requires a minimum of 90 Gb sequence data per sample.

Exome Sequencing

The selective capture and sequencing of coding regions in the genome is a powerful and cost effective tool for researchers wanting to identify disease-causing mutations. This Platform uses TrueSeq Exome Enrichment Kit (Illumina) which is an in-solution sequence capture method for isolating exonic regions of interest in the human genome. It enables systematic detection of common and rare variants by massively parallel sequencing. Typically, about 5 Gb of paired end sequence data per sample is required to sequence human exome at a mean depth of 30X.

Targeted Resequencing

A comprehensive understanding of genetic variants that influence predisposition and risk of disease is now possible. Methods combining GWAS and massively parallel sequencing can identify a full spectrum of common and rare variants implicated in a wide spectrum of phenotypes. This Platform uses highly multiplexed PCR amplification of focused genes followed by massively parallel sequencing. Each gene is amplified by multiple overlapping amplicons using 10 ng of genomic DNA. The DNA libraries are pooled and sequenced in Ion Proton and Ion Torrent PGM (Life Technologies).

Metagenomics

There is a growing recognition of the human microbiota influencing nutrition, development and disease. Massively parallel sequencing has revolutionized microbiome profiling. There are two main methods of characterizing the microbiota that do not rely on culturing these microorganisms – amplification and sequencing of 16s rRNA gene sequences and shotgun sequencing of community DNA. This Platform uses the long read GS FLX (Roche-454) for sequencing of 16s rRNA gene amplicons and shotgun DNA libraries.

Transcriptome Analysis

The transcriptome of an organism can be analyzed in great depth allowing investigation all transcriptional activity, coding and non-coding, to be investigated. Transcriptome analysis consists of determination of the relative abundance of poly-A transcripts, discovery of transcript isoforms, and characterization of splice junctions. Typically, for human transcriptome analysis, this application requires about 80 to 100 million paired end reads per transcriptome, generated from rRNA depleted and/or poly-A+ enriched RNA. Paired end 100 bp sequencing is performed using HiSeq-2500 and 2000 (Illumina). Alternatively, targeted RNA-Seq data is generated using Ion Torrent (Life Technologies).

Microarray

This Platform consists of complete laboratory set up for processing Illumina bead arrays which are scanned in iScan (Illumina) and the data analyzed in Genome Studio. The applications of this technology are:

Genome wide Genotyping

Genome wide genotyping studies are undertaken to identify common variants which might be associated with various traits. In these studies, SNP markers ranging from 715,000 to 4.5 million in number are genotyped in each DNA sample using Omni series of arrays (Illumina). The raw data can be used for genotype calling as well as copy number analysis. Studies focusing on variants in the coding region of the genome are undertaken by using Exome Beadchips for interrogating over 240,000 loci located in the human exome.

Genome wide Gene Expression

Whole genome expression profiling is a powerful method for understanding disease biology. Direct hybridization assays with Human HT12 expression beadchips (Illumina) are used to study expression of over 47,000 coding and non-coding transcripts and known splice variants across the human transcriptome.

Genome wide Methylation

Quantitative interrogation of methylation sites at single nucleotide resolution is used to identify epigenomic modifications involved in human health and disease. DNA samples are treated with Sodium Bisulfite and then subjected to genotyping with HumanMethylation450 Beadchips (Illumina) which cover more than 485,000 methylation sites across 99% of RefSeq genes and 96% of CpG islands.

Multiplex Suspension Array

Data is generated for immunoassays, receptor-ligand assays, nucleic acid hybridization assays and enzyme assays using Bioplex–200 Suspension Array (Biorad).

 

Dry Lab Activities

Genomics experiments required to solve modern problems in biology are mostly complex and highly data-intensive thus creating major challenges in analysis and interpretation of experimental data. This Platform provides a wide variety of services which aim to remove such bottlenecks in genomics research.

Project design

Contemporary research studies on genomics of human health and disease generate big data and are expensive in nature. Optimal study design and adopting efficient work strategy not only maximizes the chances of success, they can also enable cost effective generation of valuable scientific information. Consultations are provided in these areas.

Data Analysis

The biggest challenge of genomics research lies in meaningful and intelligent analysis of the large and complex data sets generated by the cutting edge techniques like massively parallel DNA sequencing and genome wide analysis. This Platform provides services for QA/QC, mapping, variant calling, quantitative analyses of gene expression and methylation, statistical analyses etc. of such experimental data.

 

 

Members

Dr. Arindam Maitra

Bijan Bhushan Bairagya

Sumanta Sarkar

Swati Jaiswal

Contact Us

Core Technologies Research Initiative
National Institute of Biomedical Genomics
Netaji Subhas Sanatorium – 2nd Floor
PO: NSS, Kalyani, District Nadia
West Bengal, India 741251
Tel: +91-33-25892151
Cell No.: +91-9903380808
Fax: +91-33-25892150