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Taking a user snapshot
OXFORD, United Kingdom—Oxford Gene Technology (OGT), a provider of genetics research and biomarker solutions for molecular medicine, has released the results of a survey of researchers using next-generation sequencing (NGS).
Designed to investigate current trends in NGS usage and determine future demands, the survey was intended to help OGT to deliver high-quality, up-to- date services and to provide insightful, relevant customer resources. The company received 596 responses from its worldwide database of contacts, and donated to the U.K. charity DEBRA (for the genetic skin blistering condition Epidermolysis Bullosa) for each completed survey.
The respondents were predominantly from academic research departments, who made up over 70 percent of the results, according to Stephen Archibald, director of communications at OGT. The next-largest category was healthcare, at 19 percent, reflecting how NGS is becoming increasingly popular within clinical research.
"We were pleasantly surprised to see the high percentage of researchers favoring targeted resequencing (46 percent) methods (whole-exome and targeted-panel sequencing) over whole-genome sequencing (13 percent)," Archibald says. "Researchers are clearly identifying the benefits of targeted resequencing, including cost-efficiency and increased depth of coverage, which improves the chance of finding biologically relevant variants."
The top three research areas for NGS were cancer (27 percent), rare disease (17 percent) and developmental disorders (15 percent). These application areas fit well with the use of targeted sequencing, particularly targeted panel sequencing, according to Archibald. He adds that targeted panel sequencing "is the tool of choice for the development of clinically focused assays," because of its cost efficiency and sensitivity.
"As the use of targeted panels increase, we expect to see more emphasis being placed on bait design optimization," Archibald adds. "This is another area where service providers such as OGT can help researchers ensure the delivery of sensitive and reproducible results."
For example, the company's SureSeq Solid Tumor Panel has been designed in conjunction with leading cancer researchers and, "through OGT's probe design algorithms, provides exceptional uniformity of coverage," Archibald says. "Based on the results provided in this survey, we will be launching new targeted sequencing panels covering additional research areas and re-emphasizing how our custom panel design, together with our sequencing service, can benefit researchers."
Bioinformatics is identified as the biggest barrier to NGS usage (56 percent), and as a consequence, 36 percent of respondents are outsourcing this key stage of the process, Archibald reveals. As sequencing capacity increases and reagents costs decrease, the pressures on in-house bioinformatics resources are becoming more apparent than ever.
"As a genomic services provider that delivers not just high-quality data, but a fully annotated interactive report that enables researchers to rapidly identify meaningful results without in-house bioinformatics resource, this finding very much aligns with our offering," Archibald says. "However, based on the survey data, there are clearly still a number of researchers with data analysis challenges who have yet to experience the benefits of outsourcing."
Survey respondents cited data quality and bioinformatics expertise among the top three essential factors when choosing an NGS service provider. Further insights into the use of NGS for clinical tests, preferred NGS methods and demands on service providers are also presented in the survey.
OGT regularly conducts market research surveys to attempt to offer customers the most appropriate technology and applications to meet their research goals. In addition, by identifying the challenges faced by researchers, the company can develop customer information that helps to ensure informed decision making.
"This survey has directly led to the creation of our recent demo version of our reporting software, showing customers how easy it can be to identify meaningful results without having to rely on an internal bioinformatics resource," Archibald says. "In addition, we use the data from such surveys to drive our webinar program, ensuring that the content is aligned with researchers' needs."
The October webinar directly addressed the challenges of custom bait design for targeted NGS panels. The survey adds to a growing portfolio of resources from OGT on NGS, including a recent white paper on choosing the right NGS method and a free-to-download demo version of the company's Genefficiency NGS reporting software.