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EXCLUSIVE – Understanding Next Generation Sequencing

OG: In your own words, can you describe what Next Generation Sequencing (NGS) is? How is it different from first generation sequencing?

WM: Genome sequencing was initially developed by Fredrick Sanger in the 1950s. Since then, several new methods for genome sequencing have been developed and these were categorized as Next Generation Sequencing (NGS). NGS builds upon Sanger’s foundation to yield accurate and cost-effective sequencing results. It is highly scalable, and a whole genome could be sequenced in a reasonable amount of time thanks to parallel analysis and high throughput technology.

The main difference between first generation sequencing and NGS is that NGS is highly scalable, and a whole genome could be sequenced in a reasonable amount of time. To put it into perspective, the first human genome that was sequenced cost about 100 million dollars, but now sequencing an entire genome costs between $300 and $1,000 depending on the sequencer used.

 OG: Walk us through the analytical process of NGS.

WM: NGS starts with a “wet phase” which means extracting the DNA material from the cells. This material consists of base pairs of the 4 bases (adenine, guanine, cytosine, and thymine). This material is then cut into pieces of specific length that varies between about 100 and 500 base pairs depending on the sequencer used.  A sequencer is mainly a high-resolution scanner that now takes tiff images of the material using various light frequencies.

In the “dry phase” – or in other words, in the computer – those snips are aligned to the whole sequence.  In case of human genome, the assembly phase is done by aligning the snips to the reference genome. The next step is finding variants, i.e. differences to the standard.  Those variants are interpreted to understand amongst others, miss-functions or diseases.

 OG: What has been the take up of NGS in hospitals globally? Which region is most enthusiastic? What are the initiatives they are working on?

 WM: According to research, the global NGS market size is estimated to register a CAGR of 20.5% from 2017 to 2022 to reach $12.45 billion by 2022. Asia Pacific is expected to register the highest growth rate during the forecast period from 2017 to 2022, due to the improving healthcare infrastructure and favourable government initiatives in this region. This speaks volumes about the adoption of NGS.

Dell EMC works with its ecosystem of healthcare partners around the world to deliver powerful and versatile compute and storage products for healthcare and life sciences organizations that want to efficiently manage clinical and genomics data, and today we see mostly two main use cases for NGS.

Firstly, Cohort Sequencing, which are country-wide or region-wide research projects to gather between 10, 000 and 100, 000 genomes of humans who are relatively similar.  The variants in their genomes enable new scientific discoveries and insights and enable setup genomic medicine services.

Secondly, Clinical Genomics used primarily in cancer treatment (oncology), heart disease (cardiology) and diabetes treatment.  This is to create a personalized treatment for patients taking the genomic differences of a patient in account.  The goal is to provide a patient with a more efficient treatment.

OG: Hospitals working in silos is a big challenge for improving NGS. This is possibly a legal issue related to privacy and security. Do you foresee integration hurdles ever being overcome? Do you think cloud computing is the solution to this?

WM: “Data Silos” within hospitals or doctors’ offices is one of the problems the healthcare industry faces. Oftentimes, digital modalities (e.g. X-rays, MRIs or Ultra-Sound) that a hospital or general practitioner uses are introduced at a different point in time. And each of these systems (e.g. PACS, genomic databanks) comes with their own IT infrastructure including data repositories and digital archives. To use this patient data for more medical insight and assist with personalized medicine, the data from these various systems needs to be consolidated across hospitals, regions and countries.

Data privacy and security are certainly challenges that the healthcare industry must focus on. As healthcare data must be managed and stored under strict governance criteria of security, privacy, sovereignty and availability, organizations typically store them in their own secure data center or possibly work with a suitably certified healthcare specialist service provider. Public cloud is off-limits for many due to this challenge.

Solutions that we advise customers to consider are using a scale-out NAS (Dell EMC Isilon) or a modern object-storage platform (Dell EMC ECS) that brings cloud scale and economics to their data centers. On-premise systems can be used to implement a ‘private cloud’ of object storage within customers’ data centers, and organizations get to retain complete control over the security and physical location of their data – all while enjoying the advantages of public cloud-like scalability, flexibility and object storage.

OG: Finally, what are some IT challenges NGS faces at present?

WM: NGS faces a few challenges including data sharing between organizations and sometimes countries, as well as adherence to data regulations. But one of the biggest challenges is managing the sheer amount of data being generated.

Most life sciences workflows containing NGS include data generation, analysis and archiving stages. Each of these stages has unique capacity and performance needs, and companies performing NGS usually require sequencing to run 24/7. It is important that organizations ensure the right production performance and that storage tiers are available as needed.

Furthermore, for organizations with longer IT procurement cycles, it is a struggle to ensure that the IT purchase process keeps up with the storage needs of the exponentially growing data produced from NGS processes. Organizations must plan for today as well as the future to meet the demanding customer needs.

They must also ensure that they are not only smart but also cost efficient with their storage solutions. The challenge is to find a versatile storage solution to balance their capacity and performance requirements that even vary over time.

One of the ways Dell EMC helps our customers overcome this is via the continuous evolvement of our Isilon platform to make sure that our life sciences customers have a solution to run NGS non-stop and achieve faster time to insights.

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