StudiesNext Generation Sequencing  As a follow-up to our recently published comprehensive study on Genomic Technologies, which covered everything from real-time PCR to microarrays, The Science Advisory Board® is pleased to release the results from our recently conducted study on Next Generation Sequencing (NGS). Next generation sequencing systems are the newest breed of sequencing instruments. These systems generate enormous amounts of sequencing data, which in the hands of a skilled researcher can be a very powerful tool for biological discovery. NGS refers to a collection of sequencing technologies that generate sequence read data in a “high throughput” and “parallel” manner. NGS technologies generally have shorter read-lengths than traditional Sanger sequencing, but read each nucleotide at deeper “coverage”. That is, while Sanger sequencing may read a region of a gene once, Next-Generation technologies can sequence this area many times over and rely on a mosaic of short sequences patched together to create a consensus sequence. An amusing look at the benefits and limitations of assembling next-generation Sequencing data can be found in the blog post written by an SAB member, Dr. Richard Wintle: “Genome Assembly – a primer for the Shakespeare fan”. In order to understand how researchers are using this emerging technology, The Science Advisory Board hosted a study to learn about how its members perceived the benefits and drawbacks of NGS technologies and to learn about how they are incorporating this new tool into their workflow. Selected results from this study are shown below. In order to learn about the drawbacks of NGS, we asked respondents to indicate the aspects of the technology they perceive as the “most limiting”. Not surprisingly, the cost of the instrument and reagents was noted as the most limiting aspect, as some sequencers can cost upwards of $1 M USD.  Beyond the cost limitation of NGS technologies, researchers indicated a variety of other limitations that provide an enormous amount of intuition about the NGS market. While the technique is very powerful when properly applied to certain applications; there are significant technical drawbacks that are limiting its utility in many situations. For example, while NGS sequencing boasts very high accuracy rates due to their high genome coverage ratios, the short read lengths produced can be difficult to align and very limiting for de novo whole genome sequencing. Researchers are instead using traditional methods (Sanger sequencing) to produce longer reads which, when combined with high coverage NGS data, can produce more accurate whole genome sequences. This small example, combined with the data above, illustrate one of the key problems with current next generation sequencing platforms. Given these drawbacks for NGS technologies, we asked researchers to indicate the applications where they were currently using NGS in their workflows. The application areas noted are shown in the chart below.  Because NGS can be tailored to deeply sequence into a very short portion of a gene, it can be a very powerful tool for revealing single nucleotide polymorphisms (SNPs). In addition NGS can be used to measure low-frequency SNPs in a tumor sample, making NGS ideal for researching tumorigenesis. It was not surprising, therefore, that we found the cancer research as one of the most common research area of interest among researchers employing NGS. While oncology applications are a natural fit for NGS data, many other applications benefit from NGS’s ability to collect enormous amounts sequence data from samples. Researchers performing genome sequencing and function, disease association studies and comparative genomics all leverage the large databases of sequence information created by NGS to draw inferences about biological function.  The adoption of NGS technologies can be a daunting task. Researchers may need to purchase expensive instruments, reagents, and data analysis tools and information gathering is essential to researching these products. In addition, they need to re-examine the value of differing kinds of sequence information that traditional and next-generation technologies produce and incorporate this new tool into their workflows. Given this level of complexity, it is not surprising that researchers who are looking to adopt NGS technologies most frequently rely on their colleagues for the information they need when evaluating NGS product offerings. We invite you to participate in our discussion about this study in our Community Forum. For questions or comments, please contact Greg Thompson at g.thompson@scienceboard.net [ View Current & Future Studies ] [ View Past Studies ] |
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