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.
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 cost of reagents and consumables required for running your samples and generating the data. There are no hidden costs. Consultations on data analysis are also provided. Anyone intending to use any of these platforms must plan their work in consultation with us (firstname.lastname@example.org, +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.
Massively-parallel, Ultra High-throughput DNA Sequencers
> NovaSeq 6000 (Illumina)
> HiSeq2500 (illumina)
Moderately High-throughput DNA Sequencing Platform
> Ion Torrent PGM (Life Technologies)
> Ion Proton platform (Life Technologies)
Genome wide Genotyping Platform
> iScan (Illumina)
Real-Time PCR Platform
> QuantStudio 7Flex (Applied Biosystems)
Capillary Sequencing Platform
> ABI 3500XL (Life Technologies)
Multiplex Suspension Array Platform
> Bio-Plex 200 (Bio-Rad)
- Automated DNA/RNA Purification Platform
> QIAsymphony SP (QIAGEN)
- DNA/RNA QA/QC platforms
> Bioanalyzer 2100 (Agilent Technologies)
>TapeStation 2200 (Agilent Technologies)
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
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 NovaSeq-6000, HiSeq-2500 (Illumina), Ion Proton and Ion Torrent PGM (Life Technologies) and 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.
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.
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 HiSeq-2500 (illumina), Ion Proton and Ion Torrent PGM (Life Technologies).
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 HiSeq-2500 (illumina) for sequencing of 16S rRNA gene amplicons and shotgun DNA libraries.
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 50 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 NovaSeq-6000 and HiSeq-2500 (illumina).
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) and Infinium Global Screening Arrays (GSA) (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 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 Methylation EPIC Beadchips (Illumina) which cover more than 8,50,000 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).
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.
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.
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.
User Charges for Common Applications:
Please note that the applications listed below are not exclusive. We will be happy to help you in case the application you require is not listed below e.g. targeted resequencing. Please provide us with details by email and we will estimate the costs and get back to you.
Dr. Arindam Maitra
Dr. Shahnaz Ali