You are a translational research scientist, clinical pathologist, or laboratory test developer, always on the lookout for new tools, best practices, the latest news, and quality information. Your daily work impacts people’s heath, which is why you entered the field in the first place, and you have seen tremendous change in the past few years with breakthrough genomic technology increasingly blurring the lines between research and ‘the clinic’.
Your information sources have started to change over time. It wasn’t that long ago when your main sources of information for your professional career were textbooks and primary literature in printed journal form, as well as professional communications such as hallway conversations or meeting a collaborator at a conference. Recently new avenues for information have opened up, richly supplementing the older sources, such as the use of internet search, email newsletters, online commentary on blogs, and online video.
Here at Genomic Precision we will be focusing on the world of precision medicine, defined as treating “a person based on [his or her] own genetic material, to enable us to provide individualized, personalized and precise care”. A key underpinning to this approach has been the revolutionary changes in genetic and genomic analysis over the past decade, with the advent of what is colloquially known as ‘Next-Generation Sequencing’ (NGS). With the first of the new generation of approach to DNA sequencing since Fred Sanger’s method invented in 1977, the 454 GS20™ instrument (454 is now a division of Roche Incorporated) produced an astonishing 100 million base-pairs of sequence in a single 10-hour run, at an unprecedented cost which was a fraction of the Sanger sequencing method.
In the ensuing years the next-generation sequencing technologies have rapidly iterated and have become much easier to use and implement. The GS20 instrument which cost $500,000 USD to purchase can be replaced with the purchase of a Thermo Fisher Scientific Ion Torrent PGM™ for $80,000 instead. Rather than spending $5,000 for a PicoTiter™ plate and associated reagents for a GS20 run, $300 can purchase an Ion 314™ chip and reagents for the Ion Torrent PGM. And instead of taking two days (1 day for template preparation and 10 hours running time) on the GS20, the time is now reduced to one day (4 hours for template preparation and 5 hours running time) for the Ion Torrent PGM.
Thus there have been major inroads of NGS as a laboratory-developed test into the clinical setting in the past 5 years, first within the established realm of clinical genetics, with multi-gene analysis of samples suspected of genetic disorders now commonplace. Instances of whole-exome sequencing to help solve the ‘diagnostic odyssey’ are commonly reported.
There are two other clinical fields on which NGS has had major impact: first with oncology (personalizing care by matching somatic tumor mutations from an individual to a therapeutic decision) and non-invasive prenatal testing (analyzing maternal blood for the fetal DNA fraction and analyzing that fraction for aneuploidy). Other emerging clinical applications include pre-implantation genetic diagnosis and monitoring of residual disease using cell-free DNA.
Yet with all the impact NGS has had, our focus on precision medicine will not be limited by that particular technology, powerful as it is. Digital PCR is increasingly adopted for examining specific mutations in cell-free DNA, and real-time PCR approaches do have their place in addition to traditional Sanger sequencing in the realm of precision medicine.
Here at the SeraCare Genomic Precision blog you can expect to find news from the research world that affects routine clinical testing; hear from key researchers and developers in this exciting field; learn about the impact regulatory decisions have on the clinical laboratory; discover journal articles relevant to your laboratory and environment; and explore aspects of the rapidly-changing world of genetic analysis that has impact on the practice of precision medicine.
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Author: Dale Yuzuki is the Director of Market Development at SeraCare Life Sciences. More information about him is available here.