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A full next-generation sequencing ecosystem could be a realistic alternative if the clinical laboratory is large or part of a larger institution.
Next-Generation Sequencing (NGS) is not yet comparable to PCR because it is a practical method for an individual to purchase their own machine. Instead, an institution is more likely to make the necessary investments and own the platform. Before making this purchase, consider the following: What do researchers hope to gain from the sequencing? The answer could be any of several possibilities. This may need the laboratory purchasing second-and third-generation NGS platforms and the necessary library preparation, storage, and bioinformatics expertise.
For RNA sequencing, there are a variety of NGS options available, each with its own set of requirements for the output data. Because of its low cost and high throughput, Illumina's NovaSeq 6000, a sequencing platform may most effectively measure transcript abundance. Because of the combination of lengthy reads and high accuracy, SMRT (Single Molecule, Real-Time) sequencing on a Pacific Biosciences technology may be ideal for sequencing the complete transcript and isoforms.
Like the Ion Torrent Genexus system, one of a kind first turnkey NGS solution combining platforms may be the most beneficial way to avoid massively complex and expensive NGS ecosystems. A full NGS ecosystem could be a realistic alternative if the clinical laboratory is large or part of a larger institution. If that is the case, combining Illumina's MiSeq with NextSeq 2000 would allow for faster sequencing of fewer samples.
Several epigenetic alterations occur within complex genomes, but the characterization of cytosine methylations to generate 5-methyl cytosine is arguably the most studied. This may be investigated by sequencing the entire genome using Illumina's NovaSeq 6000, then treating the material with bisulfite and sequencing it again. This would expose all methylations throughout the genome, but it would cost twice as much as whole-genome sequencing. Instead, the Ion Torrent system could be used to solely focus on a subset of cytosines, meaning methylated DNA would be selected for by affinity enrichment or enzymatic compartmentalization using methylation-sensitive enzymes.