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These technologies generally can be grouped into three approaches: polymerase chain reaction (PCR), hybridization, and next-generation sequencing (NGS). [22] Currently, a lot of PCR and hybridization assays have been approved by FDA as in vitro diagnostics. [47] NGS assays, however, are still at an early stage in clinical diagnostics. [48]
Helix uses NGS to sequence a proprietary assay called Exome+, a version of Exome sequencing which according to the company provides 100 times more data than was previously available. [9] Exome+ includes all 22,000 protein-coding genes as well as additional regions known to be of interest. [ 10 ]
Moreover, for pathogen sequencing the use of controls is of fundamental importance ensuring mNGS assay quality and stability over time; PhiX is used as sequencing control, then the other controls include the positive control, an additional internal control (e.g., spiked DNA or other known pathogen) and a negative control (usually water sample). [2]
Illumina also uses the DNA colony sequencing technology, invented in 1997 by Pascal Mayer and Laurent Farinelli [8] and which was acquired by Solexa in 2004 from Manteia Predictive Medicine. It is being used to perform a range of analyses, including whole genome resequencing, gene-expression analysis, and small ribonucleic acid (sRNA) analysis.
Exact Sciences Corp. is an American molecular diagnostics company based in Madison, Wisconsin specializing in the detection of early stage cancers. The company's initial focus was on the early detection and prevention of colorectal cancer; in 2014 it launched Cologuard, the first stool DNA test for colorectal cancer.
SOLiD applies sequencing by ligation and dual base encoding. The first SOLiD system was launched in 2007, generating reading lengths of 35bp and 3G data per run. After five upgrades, the 5500xl sequencing system was released in 2010, considerably increasing read length to 85bp, improving accuracy up to 99.99% and producing 30G per 7-day run. [10]
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Single-molecule RNA FISH assays can be performed in simplex or multiplex, and can be used as a follow-up experiment to quantitative PCR, or imaged simultaneously with a fluorescent antibody assay. The technology has potential applications in cancer diagnosis, [19] neuroscience, gene expression analysis, [20] and companion diagnostics.
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