February 28, 2024

We are creating some awesome events for you. Kindly bear with us.

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.

PARTNER

Qlik’s vision is a data-literate world, where everyone can use data and analytics to improve decision-making and solve their most challenging problems. A private company, Qlik offers real-time data integration and analytics solutions, powered by Qlik Cloud, to close the gaps between data, insights and action. By transforming data into Active Intelligence, businesses can drive better decisions, improve revenue and profitability, and optimize customer relationships. Qlik serves more than 38,000 active customers in over 100 countries.

PARTNER

CTC Global Singapore, a premier end-to-end IT solutions provider, is a fully owned subsidiary of ITOCHU Techno-Solutions Corporation (CTC) and ITOCHU Corporation.

Since 1972, CTC has established itself as one of the country’s top IT solutions providers. With 50 years of experience, headed by an experienced management team and staffed by over 200 qualified IT professionals, we support organizations with integrated IT solutions expertise in Autonomous IT, Cyber Security, Digital Transformation, Enterprise Cloud Infrastructure, Workplace Modernization and Professional Services.

Well-known for our strengths in system integration and consultation, CTC Global proves to be the preferred IT outsourcing destination for organizations all over Singapore today.

PARTNER

Planview has one mission: to build the future of connected work. Our solutions enable organizations to connect the business from ideas to impact, empowering companies to accelerate the achievement of what matters most. Planview’s full spectrum of Portfolio Management and Work Management solutions creates an organizational focus on the strategic outcomes that matter and empowers teams to deliver their best work, no matter how they work. The comprehensive Planview platform and enterprise success model enables customers to deliver innovative, competitive products, services, and customer experiences. Headquartered in Austin, Texas, with locations around the world, Planview has more than 1,300 employees supporting 4,500 customers and 2.6 million users worldwide. For more information, visit www.planview.com.

SUPPORTING ORGANISATION

SIRIM is a premier industrial research and technology organisation in Malaysia, wholly-owned by the Minister​ of Finance Incorporated. With over forty years of experience and expertise, SIRIM is mandated as the machinery for research and technology development, and the national champion of quality. SIRIM has always played a major role in the development of the country’s private sector. By tapping into our expertise and knowledge base, we focus on developing new technologies and improvements in the manufacturing, technology and services sectors. We nurture Small Medium Enterprises (SME) growth with solutions for technology penetration and upgrading, making it an ideal technology partner for SMEs.

PARTNER

HashiCorp provides infrastructure automation software for multi-cloud environments, enabling enterprises to unlock a common cloud operating model to provision, secure, connect, and run any application on any infrastructure. HashiCorp tools allow organizations to deliver applications faster by helping enterprises transition from manual processes and ITIL practices to self-service automation and DevOps practices. 

PARTNER

IBM is a leading global hybrid cloud and AI, and business services provider. We help clients in more than 175 countries capitalize on insights from their data, streamline business processes, reduce costs and gain the competitive edge in their industries. Nearly 3,000 government and corporate entities in critical infrastructure areas such as financial services, telecommunications and healthcare rely on IBM’s hybrid cloud platform and Red Hat OpenShift to affect their digital transformations quickly, efficiently and securely. IBM’s breakthrough innovations in AI, quantum computing, industry-specific cloud solutions and business services deliver open and flexible options to our clients. All of this is backed by IBM’s legendary commitment to trust, transparency, responsibility, inclusivity and service.

Send this to a friend