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Scientists employ genetic analysis approaches across a diverse range of research areas. Popular techniques include microarrays, sequencing, real-time PCR and other related methodologies. These techniques are used for different applications such as gene expression, genotyping, genome wide association studies, copy number variation and many more. Watson and Crick’s pioneering discovery of the structure of DNA was the birth of modern genetics, and over the past 57 years the tools used to study genetics have exploded with the invention of microarrays in the late 1980s and highlighted by the use of Sanger sequencing to sequence the human genome in 2000. The field of genetic analysis continues to grow as new tools and techniques, such as next generation sequencing, and new discoveries, such as epigenetic regulation and RNAi help to deepen our understanding of genetics and make such experiments easier and more accessible to all scientists. The advancement and accessibility of these technologies have progressed to the point where personal genome sequencing is now even beginning to be used for clinical applications. The power of this technique was recently highlighted by the high-profile Nicholas Volker case where genome sequencing helped physicians diagnose and treat a rare disease caused by a previously undiscovered genetic anomaly. Inevitably, as the costs associated with performing genomic research continue to decrease, new discoveries and applications will continue to emerge at an ever-increasing rate.
In response to these dynamics, The Science Advisory Board conducted a study of its members to learn about the techniques researchers are using to approach these kinds of studies. We interviewed nearly 500 industrial and academic scientists from around the world, and the results of this study are presented below.
The most common type of genetic analyses performed includes gene expression analysis, genotyping and gene regulation analyses. The prevalence of these techniques is not unexpected as the technologies to study these topics are generally more mature – and each can be probed by multiple technologies (e.g., microarrays, PCR, blotting), whereas other types of analyses (e.g., epigenetic analysis, targeted sequencing, de novo sequencing and SNP discovery) require more specialized and expensive instrumentation to perform.
Since the tools available to researchers in this field are changing at such a rapid pace, we sought to catalog the current technologies used and to determine the techniques researchers expected to adopt within the next two years. Not surprisingly, the most prevalent techniques used are real-time PCR, reverse transcriptase-PCR, Sanger sequencing, microscopy and microarrays. However, when asked which technique they expect to adopt within the next two years, 28% of researchers indicated next-generation sequencing, with the next largest percentage of researchers indicating they would next adopt microarrays (16%) and FISH (14%) into their genetic analysis workflow. These results seem to indicate a technology transition occurring in genetic analysis laboratories as the most established techniques (e.g., PCR based assays, blots and microscopy) have saturated most laboratories, leaving newer generation techniques more opportunity for adoption. Microarrays are an interesting case, as they are both one of the most widely currently used techniques and are one of the technologies researchers expect to adopt in the future, presumably because of both the robustness of the technique and the rapid expansion of microarray capabilities in recent years.
Newer genetic analysis instrumentation (e.g., microarrays, sequencing platforms) tends to be extremely expensive and out of the financial reach of many labs. We asked our members whether the techniques they perform were done “in-house” or “outsourced” to either a core facility or a referral laboratory to understand the extent to which these expensive techniques are outsourced. Not surprisingly, the legacy techniques (PCR, microscopy, blotting) are generally performed in-house by researchers. However, Sanger sequencing, next generation sequencing, FISH, and microarrays are commonly outsourced to referral or core laboratories because of the prohibitive cost of these instruments as well as due to the expertise that core facilities and CROs are able to offer.
Our data appears to indicate a trend amongst genetic analysis researchers – that a battery of staple technologies are being employed to perform many of their analyses, but there is a move toward adopting newer types of complex analyses with sequencing and microarrays. Researchers are not letting a lack of direct access to the expensive machinery required for microarrays or sequencing stop their use – instead they are willing to outsource this work to core and reference laboratories where established equipment and qualified operators decrease the barriers to adoption for these emerging techniques.
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