Research Facility : Sequencing Facility
Genomics facility at THSTI
Translational Health Science and Technology Institute (THSTI) has set up First generation and Next generation nucleic acids (DNA and RNA) sequencing facility at its Faridabad campus for providing research support to its faculty and other institutes. The facility regularly performs (i) Whole genome sequencing of bacterial and viral isolates, (ii) 16S rRNA gene sequencing, (iii) Shotgun metagenomic sequencing, (iv) Targeted metagenomic sequencing (ITS and 16S rRNA), (v) Metatranscriptomic sequencing, (vi) Amplicon sequencing and (vii) Multilocus sequence typing (MLST) for known bacterial species.
Currently the facility includes two sequencing platforms: (i) MiSeq system (Illumina) and (ii) 3500 Genetic Analyzer (Applied Biosystems).
- Illumina MiSeq
The MiSeq System utilizes Illumina sequencing by synthesis (SBS) chemistry, a proven next-generation sequencing (NGS) technology responsible for generating more than 90% of the world's sequencing data. This facility provides up to 15 Gb of output with 25 million sequencing reads and 2 × 300 bp read lengths.
- ABI 3500 Genetic Analyzer
Applied BiosystemsTM 3500 Genetic Analyzer is a fluorescence based 8-capillary sequencing instrument based on Sanger DNA sequencing technology. The system has wide applications like 16S rRNA sequencing for species identification, targeted DNA sequencing, epigenetic analysis, SNP analysis and biomarker analysis. A range of cloned DNA and PCR products are analyzed with a read length of up to 1000 bp.
Till now NGS facility of THSTI has completed metagenomic sequencing of approximately 3000 biological samples. In addition, NGS facility has completed about 800 bacterial whole genome sequencing. The sequencing facility has greatly contributed in SARS-CoV-2 genome sequencing in the ongoing pandemic and its contribution has been recognized by the INSACOG.
THSTI sequencing facility has first time sequenced and reported the complete and whole genome sequences of 10 different bacterial species isolated from India (1) Faecalibacterium prausnitzii (ii) Collinsella aerofaciens (iii) Bifidobacterium longum (iv) Megasphaera elsdenii (v) Environmental toxigenic Vibrio cholerae (vi) Lactobacillus iners (vii) Lactobacillus crispatus (viii) Lactobacillus. gasseri (ix) Lactobacillus jensenii, (x) Lactobacillus johnsonii.
The BioCyc genome database collection is using the Collinsella aerofaciens strain Indica as reference strain in their MetaCyc component.