Available Services
In this section, you may browse through all services available across all National Facilities. Use the filter function to filter services by National Facility, Infrastructural Unit or category of service. In addition, you may use the text search function to search across services using key words. Please note the system will search your chosen key word either in the service title or description.
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Whole Genome Sequencing (WGS)
Whole Genome Sequencing (WGS) is a robust methodology utilized in genomics research, personalized medicine, and clinical diagnostics. It entails determining the complete DNA sequence of an organism’s genome, providing understanding of genetic makeup and insights into genetic variations, evolutionary patterns, and disease mechanisms. WGS comprises: DNA extraction, library preparation involving fragmentation of DNA and addition of adapters, and sequencing using next-generation sequencing (NGS) platforms.
Bioinformatic analysis of WGS data involves assembling sequencing reads to reconstruct the genome sequence, annotating the genome, and calling variants to pinpoint differences between the sequenced genome and a reference. Illumina DNA PCR-Free library preparation protocol combines on-bead tagmentation and PCR-free chemistry. This approach ensures uniform coverage across the genome and is suitable for human WGS, de novo assembly of microbial genomes, and tumor–normal variant calling.
Whole Exome Sequencing (WES)
Whole Exome Sequencing (WES) is a targeted approach focusing on the protein-coding regions of the genome (around 1-2%). The exome encompasses a significant portion of known disease-causing mutations, it is an affordable choice for various genetic studies where focusing on protein-coding regions suffices for research or clinical objectives.
WES begins with DNA extraction, followed by library preparation involving fragmenting DNA and adding adapters. Next is exome capture, where target-specific probes enrich DNA fragments corresponding to exonic regions, the prepared exome library undergoes high-throughput sequencing.
Bioinformatic analysis includes aligning reads to a reference genome and identifying genetic variants within exonic regions, such as single nucleotide variants (SNVs), insertions, deletions, and structural variations. In the NF Genomics protocol, TWIST Comprehensive Exome Panel is utilized, covering over 99% of protein-coding genes, with a design size of 41.2 Mb and targeting a total of 36.8 Mb, including an expanded content of RefSeq and GENCODE databases.
Amplicon sequencing for microbiome analysis (16S-ITS)
Microbiome analysis via 16S and ITS amplicon sequencing is pivotal for studying microbial community composition and diversity, spanning bacteria and fungi. The 16S rRNA gene, found in bacteria and archaea, and ITS for fungi are key markers used for taxonomic classification.
The process entails sample collection, DNA extraction, PCR amplification targeting variable regions of 16S rRNA or ITS genes, library preparation, and high-throughput sequencing. Taxonomic classification involves clustering reads into operational taxonomic units (OTUs) or amplicon sequence variants (ASVs), followed by comparison to reference databases. Diversity and community analyses assess microbial community structure using metrics like alpha and beta diversity, unveiling richness, evenness, and composition insights.
Libraries are prepared using the QIAseq 16S/ITS Panels (Qiagen), developed for sequencing 16S rRNA and ITS regions on Illumina platforms and to perform a parallel profiling of bacterial and fungal communities.