scientific research in recent times has witnessed two major
breakthroughs. A common bridge between these breakthroughs is the
next-generation sequencing technology from the US-based
The Zebrafish genome which is about half the size of the human genome,
containing about 170 crore DNA base pairs, is the first eukaryotic
genome that was sequenced by the Council for Scientific and Industrial
Research (CSIR) scientists in India. The research team at Institute of
Genomics and Integrative Biology (IGIB) generated over 89 gigabases of
DNA sequences in two months time resulting in over 20x coverage of the
Zebrafish wildtype strain genome. This humongous exercise was made
possible with the CSIR supercomputing facility at IGIB.
Another breakthrough happened when the first human genome sequencing
was completed in India by CSIR scientists. During this exercise 51
gigabase data was generated leading to 13x coverage of human genome.
Indian scientists have also successfully carried out small RNA chip
sequencing, methylation sequencing, transcriptome sequencing and
digital gene expression studies for human and non-human species.
Now what forms a common bridge between all these events is the
technology used to sequence all these genomes. The next-generation
sequencing technology from the US-based Illumina has enabled massively
parallel sequencing of millions of genomic fragments ranging from 36 to
76 base pairs, which are then mapped back to the reference genome.
Illumina’s Genome Analyzer has been adopted across genome
centers worldwide, as well as individual research labs, core and
service facilities, and biotechnology and pharmaceutical companies. The
Genome Analyzer offers the highest rate of daily output and the
simplest, most user-friendly workflow. It supports the broadest set of
applications, including those used to profile and discover novel
transcripts, to create high-resolution genome-wide maps of DNA-protein
binding sites and to sequence entire human genomes to greater than 30x
In India, Illumina launched its operation in 2005 and got its first
platform that is Bead Array installed at IGIB in 2007. Currently,
Illumina is represented exclusively in India by Premas Biotech based
out of Manesar, Gurgaon, and has more then 11 installations of its
flagship genetic analysis platforms.
Microarray-based Iscan Platforms are installed at seven centers
including a service provider named Sandor Proteomics in Hyderabad. Four
Genome Analyser platforms and a Bead Express array platform were also
installed. Sandor and IGIB have both carried out pioneering GWAS
studies using Illumina and more then 9,000 samples have been processed
till date. IGIB scientists are currently using it for genotyping and
expression analysis. Indian scientist have used Illumina for human,
plants and animal genetics studies.
“This technology has been readily acceptable to people and it
is the second generation genome analyzer in true sense,” says
Rajeev Sindhi, managing director, Sandor Proteomics, Hyderabad.
“The genome analyzer in a single run, spanning nine days, can
generate upto 50 gigabytes of data,” says Praveen Gupta, vice
president — business development, Premas Biotech, Haryana.
Currently, a couple of de-novo sequencing projects are using Genome
Analyser in India. Illumina has made immense contribution for research
in India by reducing the SNP genotyping and gene expression costs and
increasing the throughput majorly by multiplexing. Illumina offers both
custom genotyping as well as whole genome genotyping solutions.
Rahul Koul in New Delhi